Apparatus and methods for one or more wavelength swept lasers and the detection of signals thereof

ABSTRACT

An optical instrument including at least a first and second wavelength swept vertical cavity laser (VCL) sources. The wavelength sweeping ranges spanned by the first and second VCL sources may differ with a region of spectral overlap. The first and second VCL sources may be operable under different modes of operation, wherein the modes of operation differ in at least one of: sweep repetition rate, sweep wavelength range, sweep center wavelength, and sweep trajectory. A VCL source may also exhibit sweep-to-sweep variation. Apparatus and methods are described for aligning sample signal data from the first VCL and sample signal data from the second VCL to generate output digital data. The output digital data is aligned with respect to at least one of: wavelength, wavenumber, and interferometric phase. The apparatus and methods can also be used to phase stabilize successive sweeps from the same VCL source or wavelength swept source.

CROSS REFERENCE TO RELATED APPLICATIONS

This application is a continuation of U.S. Non-Provisional applicationSer. No. 15/265,429 filed on Sep. 14, 2016, which claims the benefit ofU.S. Provisional Patent Application No. 62/218,118 filed on Sep. 14,2015. The disclosures of U.S. Non-Provisional application Ser. No.15/265,429 and U.S. Provisional Patent Application 62/218,118 is herebyincorporated by reference.

FIELD OF THE INVENTION

This invention relates to the field of optical instrumentation using oneor more wavelength swept lasers along with the detection and aligning orcombining or both of signals thereof.

BACKGROUND

Various products, equipment, and instrumentation use wavelength sweptlaser technology as a source for electromagnetic emission. For example,swept source optical coherence tomography (SS-OCT), alternately calledoptical frequency domain imaging (OFDI), uses a wavelength swept laserfor interferometric imaging and ranging. Another example, infrared laserspectroscopy, uses a wavelength swept laser to perform spectroscopy.Different material systems have been used as the gain medium forwavelength swept lasers. The gain medium material, processing of thegain medium material, operating environment, and pump conditionsdetermine the optical gain characteristics and an associated upper boundon the wavelength range over which the gain medium is effective. Thedesign of the laser and reflectivity of the laser cavity mirrors alsolimit the range of wavelengths that a swept laser supports. In practice,it is often the case that a single tunable laser cannot achieve thedesired wavelength range for a given application. A solution can befound to extend the effective wavelength sweep range by combining theoutputs of two or more individual lasers.

A U.S. Pat. No. 7,324,569 B2, “Method and system for spectral stitchingof tunable semiconductor sources,” teaches a multi semiconductor sourcetunable spectroscopy system that has two or more semiconductor sourcesfor generating tunable optical signals that are tunable over differentspectral bands. The system enables the combination of these tunablesignals to form an output signal that is tunable over a combined bandincluding these individual spectral bands of the separate semiconductorsources.

A U.S. Pat. No. 7,554,668 B2, “Light source for swept source opticalcoherence tomography based on cascaded distributed feedback lasers withengineered band gaps,” teaches a tunable semiconductor laser for sweptsource optical coherence tomography, comprising a semiconductorsubstrate; a waveguide on top of said substrate with multiple sectionsof different band gap engineered multiple quantum wells (MQWs); amultiple of distributed feedback (DFB) gratings corresponding to eachsaid band gap engineered MWQs, each DFB having a different Bragg gratingperiod; and anti-reflection (AR) coating deposited on at least the laseremission facet of the laser to suppress the resonance of Fabry-Perotcavity modes. Each DFB MQWs section can be activated and tuned to laseacross a fraction of the overall bandwidth as is achievable for a singleDFB laser and all sections can be sequentially activated and tuned so asto collectively cover a broad bandwidth, or simultaneously activated andtuned to enable a tunable multi-wavelength laser. The laser hence canemit either a single lasing wavelength or a multiple of lasingwavelengths and is very suitable for swept-source OCT applications.

A U.S. Pat. No. 8,665,450 B2, “Integrated dual swept source for OCTmedical imaging,” teaches an optical coherence analysis systemcomprising: a first swept source that generates a first optical signalthat is tuned over a first spectral scan band, a second swept sourcethat generates a second optical signal that is tuned over a secondspectral scan band, a combiner for combining the first optical signaland the second optical signal to form a combined optical signal, aninterferometer for dividing the combined optical signal between areference arm leading to a reference reflector and a sample arm leadingto a sample, and a detector system for detecting an interference signalgenerated from the combined optical signal from the reference arm andfrom the sample arm.

A U.S. Pat. No. 8,687,666 B2, “Integrated dual swept source for OCTmedical imaging,” teaches an optical coherence analysis systemcomprising: a first swept source that generates a first optical signalthat is tuned over a first spectral scan band, a second swept sourcethat generates a second optical signal that is tuned over a secondspectral scan band, a combiner for combining the first optical signaland the second optical signal for form a combined optical signal, aninterferometer for dividing the combined optical signal between areference arm leading to a reference reflector and a sample arm leadingto a sample, and a detector system for detecting an interference signalgenerated from the combined optical signal from the reference arm andfrom the sample arm. In embodiments, the swept sources are tunablelasers that have shared laser cavities.

A U.S. Pat. No. 8,908,189 B2, “Systems and methods for swept-sourceoptical coherence tomography,” teaches systems and methods forincreasing the duty cycle and/or producing interleaved pulses ofalternating polarization states in swept-source optical coherencetomography (OCT) systems. Embodiments including improved buffering,frequency selecting filter sharing among multiple SOAs, intracavityswitching, and multiple wavelength bands are described. The uniquepolarization properties of the source configurations have advantages inspeckle reduction, polarization-sensitive measurements, polarizationstate dependent phase shifts, spatial shifts, and temporal shifts in OCTmeasurements.

A U.S. Pat. No. 8,873,066 B2, “System and method for improvedresolution, higher scan speeds and reduced processing time in scansinvolving swept-wavelength interferometry,” teaches a system and methodfor measuring an interferometric signal from a swept-wavelengthinterferometer by scanning a tunable laser source over two wavelengthranges, whose centers are separated substantially more than the lengthof wavelength ranges. The spatial resolution of the measurement isdetermined by the inverse of the wavelength separation between a firstand second wavelength region, as well as by the wavelength range of thefirst and second regions. An electronically tunable laser may beutilized to produce two wavelength ranges that are widely separated inwavelength. Such a system and method has wide applications to the fieldsof optical frequency domain reflectometry (OFDR) and swept-wavelengthoptical coherence tomography (OCT), for example.

A US Patent Application, US 20140268050, “Tunable laser array system,”teaches a system for swept source optical coherence tomography, thesystem including a light source emitting multiplexed wavelength-sweptradiation over a total wavelength range, the light source including Nwavelength-swept vertical cavity lasers (VCL) emitting N tunable VCLoutputs having N wavelength trajectories, a combiner for combining the Ntunable VCL optical outputs into a common optical path to create themultiplexed wavelength-swept radiation, a splitter for splitting themultiplexed wavelength-swept radiation to a sample and a reference path,an optical detector for detecting an interference signal created by anoptical interference between a reflection from the sample and lighttraversing the reference path, and a signal processing system which usesthe interference signal to construct an image of the sample, wherein atleast one of the N wavelength trajectories differs from another of the Nwavelength trajectories with respect to at least one parameter.

Various apparatus and methods using a single wavelength swept laser aredescribed next for purposes of review.

A U.S. Pat. No. 8,705,047 B2, “Optical coherence tomography imagingsystem and method,” teaches an optical imaging system that includes anoptical radiation source, a frequency clock module outputting frequencyclock signals, an optical interferometer, a data acquisition (DAQ)device triggered by the frequency clock signals, and a computer toperform multi-dimensional optical imaging of the samples. The frequencyclock signals are processed by software or hardware to produce a recordcontaining frequency-time relationship of the optical radiation sourceto externally clock the sampling process of the DAQ device.

A paper, “Doppler velocity detection limitations in spectrometer basedversus swept-source optical coherence tomography” by H. C. Hendargo, R.P. McNabb, A. Dhalla, N. Shepherd, and J. A. Izatt, Biomedical OpticsExpress, Vol. 2, No. 8, published Jul. 6, 2011, teaches a swept sourceOCT system in which phase stabilization was performed in real time withthe use of an external wavelength reference. The paper teaches that inorder to compensate for the phase errors induced by fluctuations in thedata acquisition trigger generated by the light source, an externalfiber Bragg grating with a narrow linewidth (OE Land, λo=989 nm,Δλ=0.042 nm) was used to trigger the start of the acquisition for eachwavelength sweep. The experimental apparatus for phase stabilization isshown in FIG. 2A of the paper.

A paper, “Phase-stabilized optical frequency domain imaging at 1-μm forthe measurement of blood flow in the human choroid” by B. Braaf, K. A.Vermeer, V. A. D. P. Sicam, E. van Zeeburg, J. C. van Meurs, and J. F.de Boer, Optics Express, published Oct. 5, 2011, teaches that in opticalfrequency domain imaging (OFDI) the measurement of interference fringesis not exactly reproducible due to small instabilities in theswept-source laser, the interferometer and the data-acquisitionhardware. The resulting variation in wavenumber sampling makesphase-resolved detection and the removal of fixed-pattern noisechallenging in OFDI. The paper teaches a post-processing method in whichinterference fringes are resampled to the exact same wavenumber spaceusing a simultaneously recorded calibration signal. This method isimplemented in a high-speed (100 kHz) high-resolution (6.5 μm) OFDIsystem at 1-μm and is used for the removal of fixed-pattern noiseartifacts and for phase-resolved blood flow measurements in the humanchoroid.

A paper, “Efficient sweep buffering in swept source optical coherencetomography using a fast optical switch” by A. Dhalla, K. Shia, and J.Izatt, Biomedical Optics Express, Vol. 3, No. 12, published Oct. 31,2012, further teaches the fiber Bragg grating phase stabilizationapproach of the previously mentioned 2011 H. C. Hendargo paper andteaches a buffering technique for increasing the A-scan rate of sweptsource optical coherence tomography (SSOCT) systems. Numericalcompensation technique are used to modify the signal from a Mach-Zehnderinterferometer (MZI) clock obtained from the original sweep torecalibrate the buffered sweep, thereby reducing the complexity ofsystems employing lasers with integrated MZI clocks.

A US Patent Application, US 20140028997, “Agile Imaging System,” teachesan agile optical imaging system for optical coherence tomography imagingusing a tunable source comprising a wavelength tunable VCL laser. Thetunable source has long coherence length and is capable of high sweeprepetition rate, as well as changing the sweep trajectory, sweep speed,sweep repetition rate, sweep linearity, and emission wavelength range onthe fly to support multiple modes of OCT imaging. The imaging systemalso offers new enhanced dynamic range imaging capability foraccommodating bright reflections. Multiscale imaging capability allowsmeasurement over orders of magnitude dimensional scales. The imagingsystem and methods for generating the waveforms to drive the tunablelaser in flexible and agile modes of operation are also described.

A U.S. Pat. No. 8,836,953 B2, “OCT system with phase sensitiveinterference signal sampling,” teaches an OCT system and particularlyits clock system that generates a k-clock signal but also generates anoptical frequency reference sweep signal that, for example, indicatesthe start of the sweep or an absolute frequency reference associatedwith the sweep at least for the purposes of sampling of the interferencesignal and/or processing of that interference signal into the OCTimages. This optical frequency reference sweep signal is generated atexactly the same frequency of the swept optical signal from sweep tosweep of that signal. This ensures that the sampling of the interferencesignal occurs at the same frequencies, sweep to sweep. Such a system isrelevant to a number of applications in which it is important thatsuccessive sweeps of the swept optical signal be very stable withrespect to each other.

While many applications potentially benefit from using the output frommultiple wavelength swept lasers and there is teaching on generatinglight from multiple wavelength swept lasers, there is little to nodiscussion or experimental demonstration of how to effectively detectand process the light from multiple wavelength swept laser sources. Inaddition to generating the light from multiple wavelength swept lasers,there is a need to effectively detect and combine the informationproduced by the multiple wavelength swept lasers into a useful signalthat properly merges the signals and data. The detection and merging ofsignals and data is a nontrivial component of a practical apparatus thatutilizes multiple wavelength swept lasers, especially under conditionswhere the lasers may operate at different or varying speeds, atdifferent or varying repetition rates, over different or varying sweepranges, and over different or varying sweep trajectories, or when theswept laser exhibits sweep-to-sweep variation in the wavelength sweeptrajectory. The essential apparatus and methods taught in the presentapplication solve these deficiencies of systems with multiple VCLsources or other wavelength swept sources and also teach the alignmentof the interferometric phase, the wavelength, or wavenumber of multiplesequential sweeps of a single VCL source or other single wavelengthswept source. The apparatus and methods of the present invention havebenefits in reduced computation, higher robustness to noise, and greaterflexibility in operating mode of the VCL source or other wavelengthswept source.

SUMMARY

One embodiment of the present invention is an optical instrumentcomprising a first vertical cavity laser (VCL) source configured forgenerating tuned emission over a first wavelength range to generate afirst wavelength sweep; and a second VCL source configured forgenerating tuned emission over a second wavelength range to generate asecond wavelength sweep; and an optical system configured for deliveringat least a portion of the first wavelength sweep and at least a portionof the second wavelength sweep to a sample; a reference signal generatorconfigured for receiving at least a portion of the tuned emission fromthe first wavelength sweep to generate a reference signal for the firstwavelength sweep and at least a portion of the tuned emission from thesecond wavelength sweep to generate a reference signal for the secondwavelength sweep; and a sample detector configured for detecting tunedemission from the first wavelength sweep that is affected by the sampleto generate a sample signal for the first wavelength sweep and tunedemission from the second wavelength sweep that is affected by the sampleto generate a sample signal for the second wavelength sweep; and adigitizer subsystem configured for converting the sample signal from thefirst wavelength sweep into sample digital data for the first wavelengthsweep, the sample signal for the second wavelength sweep into sampledigital data for the second wavelength sweep, the reference signal forthe first wavelength sweep into reference digital data for the firstwavelength sweep, and the reference signal for the second wavelengthsweep into reference digital data for the second wavelength sweep; andan alignment processor configured for using the reference digital datafor the first wavelength sweep and the reference digital data for thesecond wavelength sweep as input to process the sample digital data forthe first wavelength sweep and the sample digital data for the secondswept wavelength sweep to generate output digital data, wherein theresulting output digital data is aligned with respect to at least oneof: wavelength, wavenumber, and interferometric phase.

Another embodiment of the present invention is a method for aligningdigital data representing optical measurements from a sample comprisinggenerating a first wavelength sweep from the tuned emission of a firstVCL source; generating a second wavelength sweep from the tuned emissionof a second VCL source; directing at least a portion of the firstwavelength sweep and at least a portion of the second wavelength sweeptowards a sample to generate a first wavelength sweep affected by thesample and a second wavelength sweep affected by the sample; detectingthe first wavelength sweep affected by the sample to generate a samplesignal for the first wavelength sweep; detecting the second wavelengthsweep affected by the sample to generate a sample signal for the secondwavelength sweep; directing at least a portion of the first wavelengthsweep and at least a portion of the second wavelength sweep towards areference signal generator; generating a reference signal for the firstwavelength sweep from the portion of the first wavelength sweep with thereference signal generator; generating a reference signal for the secondwavelength sweep from the portion of the second wavelength sweep withthe reference signal generator; converting the sample signal for thefirst wavelength sweep into sample digital data for the first wavelengthsweep; converting the sample signal for the second wavelength sweep intosample digital data for the second wavelength sweep; converting thereference signal for the first wavelength sweep into reference digitaldata for the first wavelength sweep; converting the reference signal forthe second wavelength sweep into reference digital data for the secondwavelength sweep; computing a set of alignment parameters with analignment processor, wherein the computing uses the reference digitaldata for the first wavelength sweep and the reference digital data forthe second wavelength sweep as input; and generating output digital datarepresenting the sample from the sample digital data for the firstwavelength sweep and the sample digital data for the second wavelengthsweep, wherein the output digital data is generated using the set ofalignment parameters previously computed as input, and wherein theresulting output digital data is aligned with respect to at least oneof: wavelength, wavenumber, and interferometric phase.

Another embodiment of the present invention is an optical instrumentcomprising a set of N VCL sources configured for generating tunedemission over N wavelength ranges to generate N wavelength sweeps, whereN is a number ranging from 2-6; an optical system configured fordelivering at least a portion of each of the N wavelength sweeps to asample; a reference signal generator configured for receiving at least aportion of each of the N wavelength sweeps to generate N referencesignals; a sample detector configured for detecting tuned emissionaffected by the sample to generate N sample signals; a digitizersubsystem configured for converting the N sample signals from the Nwavelength sweeps into sample digital data for the N wavelength sweepsand converting the N reference signals for the N wavelength sweeps intoreference digital data for the N wavelength sweeps; and an alignmentprocessor configured for using the reference digital data for the Nwavelength sweeps as input to process the sample digital data for the Nwavelength sweeps to generate output digital data, wherein the outputdigital data is aligned with respect to wavelength, wavenumber, orinterferometric phase.

Another embodiment of the present invention is a method for aligningdigital data representing optical measurements from a sample comprisinggenerating N wavelength sweeps from the tuned emission of N VCL sources,where N is a number from 2-6; directing at least a portion of the Nwavelength sweeps towards a sample, wherein the tuned emission of the Nwavelength sweeps is affected by the sample; detecting the tunedemission of the N wavelength sweeps affected by the sample to generate Nsample signals; directing at least a portion of the N wavelength sweepstowards a reference signal generator; generating N reference signals,one each for each of the N wavelength sweeps; converting the N samplesignals into sample digital data for the N wavelength sweeps; convertingthe N reference signals into reference digital data for the N wavelengthsweeps; computing a set of alignment parameters, wherein the computinguses the reference digital data for the N wavelength sweeps as input;and generating output digital data representing the sample from thesample digital data for the N wavelength sweeps, wherein the outputdigital data is aligned using the set of alignment parameters previouslycomputed as input, and wherein the output digital data is aligned withrespect to at least one of: wavelength, wavenumber, and interferometricphase.

Yet another embodiment of the present invention is an optical instrumentcomprising a VCL source configured for generating tuned emission over awavelength range to generate a first wavelength sweep at a first timepoint and a second wavelength sweep at a second time point; an opticalsystem configured for delivering at least a portion of the firstwavelength sweep and at least a portion of the second wavelength sweepto a sample; a reference signal generator configured for receiving atleast a portion of the tuned emission from the first wavelength sweep togenerate a reference signal for the first wavelength sweep and at leasta portion of the tuned emission from the second wavelength sweep togenerate a reference signal for the second wavelength sweep; a sampledetector configured for detecting tuned emission from the firstwavelength sweep that is affected by the sample to generate a samplesignal for the first wavelength sweep and tuned emission from the secondwavelength sweep that is affected by the sample to generate a samplesignal for the second wavelength sweep; a digitizer subsystem configuredfor converting the sample signal from the first wavelength sweep intosample digital data for the first wavelength sweep, the sample signalfor the second wavelength sweep into sample digital data for the secondwavelength sweep, the reference signal for the first wavelength sweepinto reference digital data for the first wavelength sweep, and thereference signal for the second wavelength sweep into reference digitaldata for the second wavelength sweep; and an alignment processorconfigured for using the reference digital data for the first wavelengthsweep and the reference digital data for the second wavelength sweep asinput to process the sample digital data for the first wavelength sweepand the sample digital data for the second swept wavelength sweep togenerate output digital data, wherein the resulting output digital datais aligned with respect to at least one of: wavelength, wavenumber, andinterferometric phase to wavelength, wavenumber or phase stabilize thefirst wavelength sweep to the second wavelength sweep.

Yet another embodiment of the present invention is an optical instrumentcomprising a wavelength swept source configured for generating tunedemission over a wavelength range to generate a first wavelength sweep ata first time point and a second wavelength sweep at a second time point;an optical system configured for delivering at least a portion of thefirst wavelength sweep and at least a portion of the second wavelengthsweep to a sample; a reference signal generator configured for receivingat least a portion of the tuned emission from the first wavelength sweepto generate a reference signal for the first wavelength sweep and atleast a portion of the tuned emission from the second wavelength sweepto generate a reference signal for the second wavelength sweep; a sampledetector configured for detecting tuned emission from the firstwavelength sweep that is affected by the sample to generate a samplesignal for the first wavelength sweep and tuned emission from the secondwavelength sweep that is affected by the sample to generate a samplesignal for the second wavelength sweep; an optical clock generatorconfigured for receiving a portion of the tuned emission from thewavelength swept source to generate a clock signal; a digitizersubsystem configured for converting the sample signal from the firstwavelength sweep into a sample digital data for the first wavelengthsweep, the sample signal for the second wavelength sweep into a sampledigital data for the second wavelength sweep, the reference signal forthe first wavelength sweep into a reference digital data for the firstwavelength sweep, and the reference signal for the second wavelengthsweep into a reference digital data for the second wavelength sweep,wherein the clock signal clocks the digitizer subsystem; and wherein thedigitizer subsystem further comprises either: (a) a primary analog todigital converter, wherein the primary analog to digital converter isclocked by the clock signal, and wherein the primary analog to digitalconverter is configured to convert the sample signal for the firstwavelength sweep into the sample digital data for the first wavelengthsweep and the sample signal for the second wavelength sweep into thesample digital data for the second wavelength sweep; and a circuitcomprising a digital input, wherein the circuit is configure to acquirevia the digital input and convert the reference signal for the firstwavelength sweep into the reference digital data for the firstwavelength sweep and the reference signal for the second wavelengthsweep into the reference digital data for the second wavelength sweep;and wherein the digital input is substantially simultaneously clockedwith the primary analog to digital converter or a frequency multipliedor divided copy of the clock signal; or (b) a primary analog to digitalconverter, wherein the primary analog to digital converter is clocked bythe clock signal, and wherein the primary analog to digital converter isconfigured to convert the sample signal for the first wavelength sweepinto the sample digital data for the first wavelength sweep and thesample signal for the second wavelength sweep into the sample digitaldata for the second wavelength sweep; and a secondary analog to digitalconverter, wherein the secondary analog to digital converter isconfigured to convert the reference signal for the first wavelengthsweep into the reference digital data for the first wavelength sweep andthe reference signal for the second wavelength sweep into the referencedigital data for the second wavelength sweep; and wherein the secondaryanalog to digital converter is substantially simultaneously clocked withthe primary analog to digital converter or a frequency multiplied ordivided copy of the clock signal; and an alignment processor configuredfor using the reference digital data for the first wavelength sweep andthe reference digital data for the second wavelength sweep as input toprocess the sample digital data for the first wavelength sweep and thesample digital data for the second swept wavelength sweep to generateoutput digital data, wherein the resulting output digital data isaligned with respect to at least one of: wavelength, wavenumber, andinterferometric phase to wavelength, wavenumber or phase stabilize thefirst wavelength sweep to the second wavelength sweep.

Yet another embodiment of the present invention is an optical instrumentcomprising a wavelength swept source configured for generating tunedemission over a wavelength range to generate a first wavelength sweep ata first time point and a second wavelength sweep at a second time point;an optical system configured for delivering at least a portion of thefirst wavelength sweep and at least a portion of the second wavelengthsweep to a sample; a reference signal generator configured for receivingat least a portion of the tuned emission from the first wavelength sweepto generate a reference signal for the first wavelength sweep and atleast a portion of the tuned emission from the second wavelength sweepto generate a reference signal for the second wavelength sweep; a phasecalibration generator configured for receiving at least a portion of thetuned emission from the first wavelength sweep to generate a phasecalibration signal for the first wavelength sweep and at least a portionof the tuned emission from the second wavelength sweep to generate aphase calibration signal for the second wavelength sweep; a sampledetector configured for detecting tuned emission from the firstwavelength sweep that is affected by the sample to generate a samplesignal for the first wavelength sweep and tuned emission from the secondwavelength sweep that is affected by the sample to generate a samplesignal for the second wavelength sweep; a clock source configured forgenerating a clock signal; and a digitizer subsystem configured forconverting the sample signal from the first wavelength sweep into asample digital data for the first wavelength sweep, the sample signalfor the second wavelength sweep into a sample digital data for thesecond wavelength sweep, the reference signal for the first wavelengthsweep into a reference digital data for the first wavelength sweep, thereference signal for the second wavelength sweep into a referencedigital data for the second wavelength sweep, the phase calibrationsignal for the first wavelength sweep into a phase calibration digitaldata for the first wavelength sweep, and the phase calibration signalfor the second wavelength sweep into a phase calibration digital datafor the second wavelength sweep; wherein the clock signal clocks thedigitizer subsystem, and wherein the digitizer subsystem furthercomprises: (a) a primary analog to digital converter, wherein theprimary analog to digital converter is clocked by the clock signal, andwherein the primary analog to digital converter is configured to convertthe sample signal for the first wavelength sweep into sample digitaldata for the first wavelength sweep and the sample signal for the secondwavelength sweep into sample digital data for the second wavelengthsweep; (b) a circuit comprising a digital input, wherein the digitalinput sampling is clocked by the clock signal or a frequency multipliedor divided copy of the clock signal, and wherein the circuit isconfigured to acquire via the digital input and convert the referencesignal for the first wavelength sweep into reference digital data forthe first wavelength sweep and the reference signal for the secondwavelength sweep into reference digital data for the second wavelengthsweep; and (c) a secondary analog to digital converter, wherein thesecondary analog to digital converter is clocked by the clock signal ora frequency multiplied or divided copy of the clock signal; and whereinthe secondary analog to digital converter is configured to convert thephase calibration signal for the first wavelength sweep into phasecalibration digital data for the first wavelength sweep and the phasecalibration signal for the second wavelength sweep into phasecalibration digital data for the second wavelength sweep; and analignment processor configured for using the reference digital data forthe first wavelength sweep, the phase calibration digital data for thefirst wavelength sweep, the reference digital data for the secondwavelength sweep, and the phase calibration digital data for the secondsweep as input to process the sample digital data for the firstwavelength sweep and the sample digital data for the second sweptwavelength sweep to generate output digital data, wherein the resultingoutput digital data is aligned with respect to at least one of:wavelength, wavenumber, and interferometric phase to wavelength,wavenumber, or phase stabilize the first wavelength sweep to the secondwavelength sweep.

BRIEF DESCRIPTION OF THE DRAWINGS

FIGS. 1A-1F are drawings showing the basic principles of opticalcoherence tomography (OCT), scanning, and data formation.

FIGS. 2A-2B are schematic drawings showing example optical coherencetomography instruments.

FIGS. 3A-3D are drawings and a flowchart illustrating differences inoptical coherence tomography fringes from a mirror reflection asobtained under different operating conditions.

FIGS. 4A-4F are plots showing the effects of laser wavelength sweeptrajectory on OCT interferometric fringe frequency and fringe envelopeon the OCT point spread function.

FIGS. 5A-5D are schematic drawings showing different digitizer subsystem architectures.

FIGS. 6A-6D are plots and images showing artifacts that can occur in OCTimages due to improper background subtraction and OCT fringe jitter.

FIG. 7A is a schematic drawing of a MEMS-tunable vertical cavity surfaceemitting laser (MEMS-tunable VCSEL), FIGS. 7B-7C are photos of aMEMS-tunable VCSEL, and FIGS. 7D-7E are plots showing static and dynamicwavelength tuning of a MEMS-tunable VCSEL.

FIGS. 8A-8D are plots showing experimental spectra from MEMS-tunableVCSELs with different, but overlapping tuning range and spectra fromoptical amplifiers with different, but overlapping gain spectral range.

FIG. 9A is a plot of the frequency response of different actuatorsdesigns of MEMS-tunable VCSELs and FIG. 9B is a plot showing a vibratorymode of a MEMS-tunable VCSEL actuator.

FIG. 10A is a schematic drawing of a system combining the light from twovertical cavity lasers (VCL) sources, FIG. 10B is a plot of thewavelength vs. time of the two VCL sources executing a coordinate sweepwith a portion of the sweep turned off, FIG. 10C is a plot of thewavelength vs. time of the full sweeps, and FIG. 10D is a plot of theOCT fringe of the VCL sources individually and combined.

FIGS. 11A-11D are schematic drawings showing different methods andapparatus to combine and monitor the light from multiple VCL Sources.

FIG. 12 is a schematic drawing of electronics to drive multiple VCLs,monitor the output of the VCL sources, select the output from one of theVCL sources and amplify the optical power of the VCLs.

FIGS. 13A-13F are plots and images showing the effects of improperlycombining the interferometric fringe data from multiple VCL sources.

FIGS. 14A-14E are plots and images showing the effects of changing theposition of where two fringes are improperly combined relative to thetotal fringe length.

FIGS. 15A-15C are schematic diagrams showing an embodiment of thepresent invention comprising two VCL sources and FIG. 15D is anembodiment of the present invention comprising N VCL sources.

FIG. 16A is a schematic diagram showing an embodiment of the presentinvention comprising a VCL source and FIG. 16B is an embodiment of thepresent invention comprising a wavelength swept source.

FIGS. 17A-17C are plots showing a comparison of reference signals forthe purpose of properly aligning wavelength signals.

FIGS. 18A-18D are plots showing identification of a sample offset valueto properly align two wavelength signals.

FIGS. 19A-19I are schematic diagrams and plots showing example referencesignal generators of the present invention.

FIGS. 20A-20D are plots showing the effects of different optical filterdesigns on the alignment process of one embodiment of the presentinvention.

FIG. 21 is a schematic diagram showing an embodiment of the presentinvention that comprises two analog to digital converters, an opticallyderived k-clock signal generator to clock the analog to digitalconverters, and an electrical trigger signal.

FIGS. 22A-22E are plots showing proper data alignment from an embodimentof the present invention that comprises a Fabry-Perot filter basedreference signal generate, two analog to digital converters, anoptically derived k-clock signal to clock the analog to digitalconverters, and an electrical trigger signal.

FIG. 23A is a schematic diagram and FIG. 23B is a plot showing areference signal generator comprising two etalons of different length,two detectors, and an electrical summing circuit.

FIG. 24A is a schematic diagram of a reference signal generatorcomprising two etalons of different length and two detectors and FIG.24B are plots showing signals from the etalons, digitized signals fromthe etalons, and a signal composed of an OR operator applied todigitized signals from the etalons.

FIGS. 25A-25F are plots showing signals from two VCL sources includingthe signals from the etalons, the digitized signals from the etalons,and a signal composed of an OR operator applied to the digitized signalsfrom the etalons.

FIG. 26A is a schematic diagram and FIG. 26B is a plot showing theoutput of a reference signal generator comprising two etalons ofdifferent length and one detector.

FIG. 27A is a screen capture from an oscilloscope of an opticalinterference signal from a VCL source, FIG. 27B is a screen capture froman optical spectrum analyzer of the spectrum of a VCL source, FIG. 27Cis a photo of a reference signal generator comprising two etalons ofdifferent length and two detectors, and FIG. 27D is a schematic diagramof a reference signal generator comprising two Fabry-Perot filters andtwo detectors.

FIG. 28 is a collection of plots showing signals from two etalons in areference signal generator.

FIG. 29 is a collection of plots showing signals from two etalonsgenerated by a single long sweep range VCL and two shorter sweep rangeVCLs with spectrums that don't overlap.

FIGS. 30A and 30C are schematic diagrams and FIG. 30B is a plot showinga comparator acting on a Fabry-Perot signal to digitally sample areference signal.

FIG. 31 is a schematic diagram showing an embodiment of the presentinvention that comprises two analog to digital converters, an internalclock signal to clock the analog to digital converters, a digital input,and an electrical trigger signal.

FIG. 32A shows a schematic diagram and FIG. 32B is a photograph of adigitizer subsystem that acquires a digital signal synchronously withthe analog data.

FIG. 33 is a diagram of an example data storage scheme for analog anddigital data.

FIG. 34 is a schematic diagram showing an experimental test apparatus ofone embodiment of the present invention.

FIG. 35A is a plot showing digital data and analog data with FIGS.35B-35D showing zoomed in plots of the digital data state transitions.

FIGS. 36A-36D are plots showing experimental data from a 1050 nm VCSELin which the analog data has been aligned to the rising edge digitalstate transition of a detected and amplified 1049 nm fiber Bragggrating.

FIGS. 37A-37D are plots showing experimental data from a 1050 nm VCSELin which the analog data has been phase stabilized and a plot of two OCTpoint spread functions plotted on top of each other.

FIGS. 38A-38B are plots showing experimental data of combining a firstsweep over a first wavelength range and a second sweep over a secondwavelength range in which the wavelength ranges overlap and FIG. 38Cshows OCT point spread functions.

FIG. 39A is a set of plots showing example reference signals foraligning sample digital data obtained at a first time point with sampledigital data obtained at a second time point obtained over the samewavelength range to generate a output digital data that is wavelength,wavenumber, or interferometric phase stabilized and FIG. 39B is acollection of plots showing example reference signals from a first andsecond VCSEL of different center wavelength in which the sample digitaldata from the first VCSEL can be combined with the sample digital datafrom the second VCSEL to generate a combined output digital data setthat is continuous in fringe phase.

FIG. 40 is a schematic diagram of one embodiment of the presentinvention comprising an optical wavelength trigger.

FIG. 41A is a schematic diagram, FIG. 41B is a data record and FIG. 41Cis a collection of plots showing pre trigger and post triggeracquisition.

FIGS. 42A-42B are plots showing a reference signal from an MZI in whichthe phase period of the signal from the MZI is larger than the triggersignal jitter due to sweep-to-sweep variation.

FIG. 43 is a collection of plots and a schematic diagram showingacquisition of the sample signal and the reference signal with differentrecord sizes.

FIG. 44A is a schematic diagram and FIG. 44B is a collection of plotsshowing one embodiment of the present invention wherein light to theinstrument is turned off while light to the reference signal generatorremains on in order to minimize light exposure to the sample while stillgenerating a reference signal that can be used for a correspondencematch.

FIGS. 45A-45B are plots showing the results after alignment from oneembodiment of the present invention wherein light to the instrument isturned off while light to the reference signal generator remains on inorder to minimize light exposure to the sample while still generating areference signal that can be used for a correspondence match.

FIG. 46 is a plot and timing diagrams showing turning a first VCL on andoff, a second VCL on and off, and a booster optical amplifier (BOA) onand off to minimize light exposure to the sample.

FIG. 47 is a schematic diagram of an embodiment of the present inventioncomprising a single or multiple VCLs, a digital input and an opticalk-clock with optional polarization selective elements.

FIGS. 48A-48D are schematic diagrams showing the joining of 2, 3, 4, orN VCL sources.

FIGS. 49A and 49C are schematic diagrams and FIGS. 49B and 49D are plotsshowing concatenation of either two or three VCL sources.

FIGS. 50A-50D are plots showing either individual or combined use of twoVCL sources to generate OCT data.

FIG. 51 is a schematic diagram of an embodiment of the present inventionthat comprises two analog to digital converters, an imaginginterferometer, a calibration interferometer, and a reference signalgenerator.

FIG. 52 is a schematic diagram of embodiment of the present inventionthat comprises two fast analog to digital converters, one slow analog todigital converter and a digital input.

FIGS. 53A-53D are schematic diagrams showing several differentconceptual ways of partitioning the components of example embodiments ofthe present invention.

FIGS. 54A-54C are schematic diagrams showing several different platformarchitectures for example embodiments of the present invention.

DETAILED DESCRIPTION OF THE PREFERRED EMBODIMENTS

The description of illustrative embodiments according to principles ofthe present invention is intended to be read in connection with theaccompanying drawings, which are to be considered part of the entirewritten description. In the description of embodiments of the inventiondisclosed herein, any reference to direction or orientation is merelyintended for convenience of description and is not intended in any wayto limit the scope of the present invention. Relative terms such as“lower,” “upper,” “horizontal,” “vertical,” “above,” “below,” “up,”“down,” “top” and “bottom” as well as derivative thereof (e.g.,“horizontally,” “downwardly,” “upwardly,” etc.) should be construed torefer to the orientation as then described or as shown in the drawingunder discussion. These relative terms are for convenience ofdescription only and do not require that the apparatus be constructed oroperated in a particular orientation unless explicitly indicated assuch. Terms such as “attached,” “affixed,” “connected,” “coupled,”“interconnected,” and similar refer to a relationship wherein structuresare secured or attached to one another either directly or indirectlythrough intervening structures, as well as both movable or rigidattachments or relationships, unless expressly described otherwise.Moreover, the features and benefits of the invention are illustrated byreference to the exemplified embodiments. Accordingly, the inventionexpressly should not be limited to such exemplary embodimentsillustrating some possible non-limiting combination of features that mayexist alone or in other combinations of features; the scope of theinvention being defined by the claims appended hereto.

This disclosure describes the best mode or modes of practicing theinvention as presently contemplated. This description is not intended tobe understood in a limiting sense, but provides an example of theinvention presented solely for illustrative purposes by reference to theaccompanying drawings to advise one of ordinary skill in the art of theadvantages and construction of the invention. In the various views ofthe drawings, like reference characters designate like or similar parts.

Review of Instrument Technology

Optical Coherence Tomography (OCT) is a non-invasive, interferometricoptical imaging technique that can generate micron resolution 2D and 3Dimages of tissue and other scattering or reflective materials. OCT isoften used for biomedical imaging or materials inspection. Firstdemonstrated for imaging the human eye and coronary arteries in 1991,OCT has since been established as a clinical standard for diagnosing andmonitoring treatment of eye disease. OCT is also used for intravascularimaging of plaque to assess heart disease, imaging of cancer,developmental biology research, art preservation, industrial inspection,metrology, and quality assurance. In general, OCT is useful forapplications that benefit from subsurface imaging, surface profiling,motion characterization, fluid flow characterization, index ofrefraction measurement, birefringence characterization, scatteringcharacterization, distance measurement, and measurement of dynamicprocesses.

FIG. 1A shows a simplified schematic diagram of a basic opticalcoherence tomography system 100. A light source 105 generates light thatis split by a beam splitter 125 into a reference arm (alternately calleda reference optical path) and a sample arm (alternately called a sampleoptical path) of an interferometer. Light is directed towards a sample115, where a portion of the light is backreflected or backscattered fromthe sample. Light from the sample is collected and combined with lightreflected by a reference mirror 110 from the reference arm. The combinedlight interferes and is detected by a detector 120 to form aninterferogram, sometimes called an OCT fringe. Processing of theinterferogram generates a reflectivity vs. depth profile of the sample,called an A-scan.

Most OCT systems include a means for scanning the light across thesample. It is possible to scan the light across the sample using a beamsteering mechanism, as shown in FIG. 1B, which has the advantage of notrequiring motion of the sample. Most commonly, steering mirrors 130 areused to steer the beam. It is also possible to move the sample itselfrelative to the OCT instrument, as shown in FIG. 1C. The OCT instrumentitself can also be moved relative to the sample for scanning the beam.At a given transverse position on the sample, the OCT system generates areflectivity vs. depth profile, or A-scan 135, as shown in FIG. 1D.Scanning the light across the sample in a single transverse directionenables the collection of multiple A-scans, which when assembled, form across sectional image, or B-scan 140, as shown in FIG. 1E. The light canalso be scanned in multiple directions to generate a 3D volume 145, asshown in FIG. 1F. Other scan trajectories are possible, such astrajectories that image areas of interest, that track or follow motionof an object, that execute circular paths, that execute spirals, thatexecute arbitrary trajectories, or that remain in one place to measure adynamic process.

The most common implementation of OCT is spectral/Fourier domain OCT,which uses a broadband light source, interferometer, and spectrometerwith a linescan camera. Light sources for spectral/Fourier domain OCThave include titanium sapphire lasers, light emitting diodes,superluminescent diodes (SLD), and supercontinuum sources, among others.In OCT, the axial resolution is inversely proportional to the bandwidthof the light source. Assuming a Gaussian spectral shape of the light,the theoretical axial resolution, Δz, is given by:

${{\Delta\; z} = {\frac{2\mspace{11mu}\ln\mspace{11mu} 2}{\pi}\frac{\lambda_{0}^{2}}{\Delta\lambda}}},$

where λ₀ is the center wavelength and Δλ is the full width half max(FWHM) of the light source spectrum.

It is often the case that a single light source does not generate aspectrum that is broad enough to generate the desired OCT axialresolution. Multiple light sources can be combined such that the outputspectrum of the light source is broader than any of the individual lightsource components alone. For example, the Broadlighter line of lightsource products from Superlum include multiple fiber coupledsuperluminescent diodes (SLD). The D series (e.g. D-840-H) includes twoSLDs, the T series (e.g. T-860-HP) includes three SLDs, and Q series(e.g. Q-1350-HP) includes four SLDs to achieve broad spectrum and highoutput power. The OCT axial resolution achievable with a multi-SLDsource is finer than the OCT axial resolution achievable with a singleSLD source alone. Thus, multi-SLD sources are highly desirable forcertain OCT applications that benefit from improved axial resolution.

An alternate implementation of OCT is swept source OCT (SS-OCT). Sweptsource OCT uses a wavelength swept laser, interferometer, diodedetector, and high speed A/D converter. FIGS. 2A and 2B show schematicdiagrams of example swept source OCT systems. The swept source OCTsystem in FIG. 2A uses fiber couplers in the interferometer. The imaginginterferometer 245 includes a sample optical path 215, a referenceoptical path 220, and path interfering element 225, and wherein theoptical instrument performs optical coherence tomography, and whereinthe output digital data is further processed into A-scans 135. The sweptsource OCT system in FIG. 2B uses circulators in the interferometer.Depending on the wavelength of operation, either a fiber coupler basedor circulator based interferometer might be preferred for efficiency.For example, circulators at 1310 nm are highly efficient, whilecirculators at 850 nm and 1050 nm are generally less efficient, making afiber coupler based implementation often preferable from a performancestandpoint and also less costly to implement.

Swept Source OCT systems operate by sweeping an emission wavelength intime, using the emission as an input to an OCT interferometer, detectingthe interferometric signal from the interferometer, and digitizing thesignal for analysis, as illustrated in FIG. 3A. For illustrativepurposes, the example fringe shown in FIG. 3A is roughly the fringepattern that would be expected from a single mirror reflection asrecorded by a Swept Source OCT system. To understand Swept Source OCTimaging principles and system limitations, it is helpful to consider theOCT signal from a mirror reflection under different imagingconfigurations. Refer to Eq. 1 below, where k_(m) is the wavenumber atsample point m, I[k_(m)] is the instantaneous photocurrent at samplepoint m, ρ[k_(m)] is the detector responsively at sample point m,S[k_(m)] is the instantaneous power on the sample at sample point m,R_(R) is the reflectivity of the reference mirror, R_(S) is thereflectivity of the sample mirror, z_(r) is the depth of the referencemirror, and z_(s) is the depth of the sample arm mirror. Equation 1 wasadapted from J. A. Izatt and M. A. Choma, Section 2.7, W. Drexler and J.G. Fujimoto Ed., “Optical Coherence Tomography: Technology andApplications,” 2008. In practice, the photocurrent, I, is generallytransformed into a voltage by a transimpedance amplifier before analogto digital (A/D) digitization.

$\begin{matrix}{{I\left\lbrack k_{m} \right\rbrack} = {\frac{\rho\left\lbrack k_{m} \right\rbrack}{2}{S\left\lbrack k_{m} \right\rbrack}\left( {R_{R} + R_{S} + {2\sqrt{R_{R}R_{S}}\mspace{11mu}{\cos\left( {2{k_{m}\left( {z_{r} - z_{s}} \right)}} \right)}}} \right.}} & {{Eq}.\mspace{14mu} 1}\end{matrix}$

The term inside the cosine function represents the phase of the OCTfringe. As the phase increases (or decreases), the OCT fringe oscillateswith a full period of oscillation occurring every 2π radians. Awavelength sweep has a starting wavenumber, k_(start), and an endingwavenumber, k_(end). The number of oscillations in the OCT fringe isproportional to the magnitude of the total phase difference, ΔΦ, overthe sweep, which is given byΔΦ=2(k _(end) −k _(start))(z _(r) −r _(s)).  Eq. 2

Equation 2 shows that the fringe frequency increases with increasingimaging depth (i.e., there is a larger number of oscillations over thesweep) because the (z_(r)−z_(s)) multiplier term inside the cosinefunction increases total fringe phase, as illustrated in FIG. 3B. Allother sweep characteristics being equal, the fringe frequency increaseswith increasing sweep repetition rate for a given mirror position, asillustrated in FIG. 3C, because the same number of fringe oscillationsoccur over a shorter time. Similarly, with all other sweepcharacteristics being equal, the fringe frequency increases withincreasing wavelength sweep range for a given mirror position, asillustrated in FIG. 3D, because the total phase difference increases dueto the larger (k_(end)−k_(start)) term. FIG. 4A shows an additionaleffect on fringe frequency in that the fringe frequency is alsodetermined by the sweep trajectory. A sweep that has slow and fastportions, such as that produced with a sine wave trajectory, has a peakfringe frequency where rate of change in wavenumber (k) vs. time isgreatest. To the designer of an OCT imaging system, the consequences ofthese effects on fringe frequency are significant because of limitationsand challenges associated with detecting and digitizing the fringe. Inorder to prevent aliasing of the fringe signal, the analog to digitalconverter (A/D) must sample at least two times as fast as the fringefrequency, according to Nyquist sampling criteria. It is thereforepreferential to linearize the sweep frequency so that the sweep islinear in k-space (wavenumber) vs. time, as shown in FIG. 4A bottom, orto more generally minimize the peak fringe frequency to maximize OCTimaging range for a given maximum digitization rate. As the samplingrate of A/D converters increases, the cost of the A/D itself increasesalong with the cost, complexity, and timing requirements of theassociated support electronics, data streaming mechanisms, and datastorage. It is therefore often not feasible to simply choose a fast A/Dconverter rate and a compromise must be made in maximum obtainable databandwidth (analog detection bandwidth, A/D rate, data streaming, andstorage) according to what the market will support for the intendedimaging application.

For a given maximum acquisition bandwidth and A/D conversion rate,tradeoffs must be made in the OCT system design between instrumentimaging range, sweep repetition rate (with associated OCT instrumentsensitivity), and axial resolution. A further consideration affectingthe OCT axial point spread function and resolution is the shape of thefringe envelope. A fringe with wide spectral envelope (FIG. 4D-1)generates an OCT axial point spread function with fine axial resolution,but large sidelobes (FIG. 4E-1). The sidelobes create artifacts or ghostimages in the OCT data. For the same total sweep range, shaping thespectral envelope to more approximate a Guassian profile (FIG. 4D-2)reduces the sidelobes, but slightly compromises OCT axial resolution.Shaping the spectral envelope further (FIG. 4D-3) produces improvedsidelobe performance, but at a cost of OCT axial resolution (FIG. 4E-3).A comparison of OCT axial point spread functions for cases 1-3 is shownin FIG. 4F.

A Swept Source OCT system acquires the interferogram with an analog todigital converter (A/D). Most modern Swept Source OCT systems usededicated A/D chips that are connected to an A/D controller. The A/Dcontroller could be a field programmable gate array (FPGA), amicrocontroller, an application specific integrated circuit (ASIC), amicroprocessor, or any other device that can communicate with an A/Dconverter. The A/D converter can communicate with the A/D controller viaany one of many communication methods, including, but not limited to: aparallel data bus, a serial data bus, direct electrical connection,optical connection, wireless connection, or other. The A/D can also beintegrated into a larger circuit. For example, many microcontrollers,microprocessors, and FPGA devices have integrated A/D converters and actas the A/D controller. FIGS. 5A-5D show schematics of possible A/Dconverter configurations. FIGS. 5A-5D are not exhaustive. For thepurposes of an embodiment of the present invention, the digitizersubsystem comprises the A/D converter 505 or multiple A/D converters,the A/D controller, and the electronics associated with the triggeringof at least one A/D converter. The digitizer subsystem can have one,two, or more channels of A/D acquisition. In FIG. 5A, the A/D chip hastwo A/D input channels and the A/D controller is an FPGA. In FIG. 5B,the digitizer subsystem comprises two A/D chips for two channels of A/Dacquisition and the A/D controller is a microprocessor (uP). In bothFIG. 5A and FIG. 5B, an A/D controller is connected to the A/D chip viaa parallel data bus. The A/D converter is clocked by either an externalclock signal or a clock derived from a source in the digitizersubsystem, referred to as an internal clock. The internal clock could bea dedicated oscillator, part of another electronics circuit, or derivedfrom any oscillatory source. The FPGA is clocked by its own clock sourcewhich may or may not be synchronous with the A/D clock source. In manyimplementations, the A/D converter remains in an active and convertingstate, continuously transmitting data to the FPGA. The FPGA monitors thetrigger input signal and based on the internal state of the FPGA and thevalue of the trigger signal determines if the recently converted A/Dvalues should be discarded or saved for processing. In an OCTapplication, it is common but not required that the digitizer subsystemremain in a ready state in which A/D converted values are discardeduntil there is a trigger event, at which time A/D converted values aresaved for processing. Generally, the A/D controller will be configuredto acquire a certain predetermined number of A/D samples upon detectinga trigger event, the number of samples being of a length appropriate tocapture a full or partial interferogram or laser sweep to form a record.A trigger event is most commonly a voltage level transition on thetrigger input, but other methods of triggering, including level basedtriggering or optical triggering can be used, amount others. Asignificant problem exists in determining the starting wavelength,wavenumber, or interferogram phase because of possible asynchronicitybetween the laser sweep, the A/D clock signal, the trigger signal, andthe clock governing the state transitions of the A/D controller.Referring to FIG. 5C, if the trigger signal is a rising or falling edgeelectrical signal synchronized with the sweep, it is possible that theedge transition of the trigger signal occurs at or near the same time asthe clock transition governing the A/D controller's sampling of thetrigger input. The A/D controller may detect the trigger transition onthe clock transition, or it may miss the trigger transition until thenext clock transition occurs. This introduces an at least one sample ofuncertainty in the starting wavelength, wavenumber, or interferogramphase in the acquired data. Electrical noise further compounds theuncertainty. If the trigger signal is a rising or falling edge signalderived from an optical wavelength detector the same problem existsbecause the optical signal could be generated at or near the same timeas the clock transition governing the A/D controller's sampling of thetrigger input. Referring to FIG. 5D, in which an optical k-clock is usedto clock the A/D converter, the same problem exists with either anelectrical trigger input or an input derived from an optical wavelengthsensor because in either case, the trigger transition may occur at ornear the same time as the clock transition.

Characteristics of the OCT interferometer and imaging system also affectthe quality of the resulting OCT image. Because of a wavelengthdependence on the splitting ratio of the fiber coupler or beam splitterthat interferes the light from the sample arm and the reference arm, thebalanced detection often used in Swept Source OCT generates a backgroundsignal, as shown in FIG. 6A. The background signal is generally composedof low frequency components that generate artifacts in the OCT imagenear the zero-delay (zero depth position). The OCT fringe is formed ontop of the background signal and it is common to subtract the backgroundsignal from the acquired data to yield the interferometric fringe, asdescribed in Section 2.4 of the book chapter by J. A. Izatt and M. A.Choma, “Optical Coherence Tomography: Technology and Applications,”2008. Further, reflective surfaces within the OCT system can generatefixed pattern artifacts. Fixed pattern artifacts are highly visible inFig. 5B of a paper, “Phase-stabilized optical frequency domain imagingat 1-μm for the measurement of blood flow in the human choroid,” by B.Braaf, K. Vermeer, V. Sicam, E. van Zeeburg, J. van Meurs, and J. deBoer, Opt. Express 19, 20886-20903 (2011). Fixed pattern artifacts arealso highly visible in Fig. 2A of a paper, “Phase-sensitive swept-sourceoptical coherence tomography imaging of the human retina with a verticalcavity surface-emitting laser light source,” by W. Choi, B. Potsaid, V.Jayaraman, B. Baumann, I. Grulkowski, J. Liu, C. Lu, A. Cable, D. Huang,J. Duker, and J. Fujimoto, Opt. Lett. 38, 338-340 (2013). Phasestabilization of the OCT fringe has been shown to remove the fixedpattern artifacts, as shown in Fig. 2B of the W. Choi (2013) paper andFig. 6C of the B. Braaf (2011) paper.

FIGS. 6B-6D show results of a simulation based on Eq. 1 that modelsthree bright reflections to represent the retina of an eye and onereflection to represent a fixed pattern reflection. The simulation wasperformed with an optical sweep from 990 nm to 1100 nm and assumesoptical k-clocking to generate 500 A/D converted samples with equalwavenumber spacing. A total of 300 OCT fringes were simulated. Torepresent the trigger jitter observed in experimental OCT systems due toasynchronous clocks and electrical noise, a sample shift of 0 samples or1 sample was randomly applied to each OCT fringe. The resulting data isshown in FIG. 6B after background subtraction. Two distinct groupings ofwaveforms can be seen. A first grouping of waveforms represents OCTfringe data with a 0 sample shift and the other grouping represents OCTfringe data with a 1 sample shift. For the case of the 0 sample shiftdata, the background and fixed pattern interference fringe is properlysubtracted. For the case of the 1 sample shift data, the subtraction ofthe background and fixed pattern interference fringe is imperfect. FIG.6C and FIG. 6D show a simulated OCT cross sectional image (B-scan) and aplot of the OCT data across the B-scan, respectively, after zero paddingand Fourier transformation of the fringe. The effects of the improperbackground and fixed pattern interference fringe subtraction generateartifacts near the zero depth position and at the depth of the fixedpattern reflection. Compare FIG. 6C of the present patent application toFig. 2A in the previously mentioned W. Choi (2013) paper and to Fig. 5Bin the previously mentioned B. Braaf (2011) paper to see the similarityin appearance and dashed nature of the background artifact and the lineassociated with the fixed pattern reflection. The W. Choi (2013) paperdescribes single channel A/D conversion using an optical k-clock togenerate the OCT fringe with equal wavenumber spacing between fringedata points. The B. Braff (2011) paper describes two channel A/Dconversion using fixed rate sampling and software resampling of the OCTfringe to generate an OCT fringe with equal wavenumber spacing betweenfringe data points, in which a Hilbert transform is used to extract thefringe phase to resample the fringe data. In both cases of the opticalk-clock and fixed rate sampling, the trigger jitter and wavelength sweepjitter create unacceptable artifacts in the resulting OCT images thatmust be appropriately managed as the papers describe.

Vertical Cavity Laser Technology

Various swept laser technologies have been used in Swept Source OCT andspectroscopy systems, including external cavity lasers based on rotatingpolygon mirrors, external cavity lasers based on galvo driven gratingfilters, Fourier domain model locked lasers (FDML), Vernier tuneddistributed Bragg reflector (VT-DBR) lasers, short cavity externalcavity lasers, and others. One particularly attractive light source formany applications is the vertical cavity laser (VCL).

A VCL is a semiconductor laser in which the direction of lasing ispredominately perpendicular to the wafer. Tuning of the wavelength oflight is accomplished by changing the optical path length of the lasercavity, which is formed by a top mirror and a bottom mirror. The opticalpath length of the laser cavity can be adjusted by changing the physicaldistance between the mirrors, changing the index of refraction of amaterial between the mirrors, or a combination of a change in both. FIG.7A shows a diagram of a specific VCL, which is a microelectromechanicalsystem (MEMS)-tunable Vertical-Cavity Surface-Emitting Laser (VCSEL), oralternately called MEMS-tunable VCSEL. The MEMS-tunable VCSEL ismanufactured using wafer fabrication techniques, as shown in FIG. 7B. Amagnified image shows a single MEMS-tunable VCSEL device from the waferas shown in FIG. 7C. In this particular design, the gain material isoptically pumped with light from an external pump laser of suitablewavelength for stimulating the gain material. The MEMS-tunable VCSELlaser cavity is formed with the gain material located between two endmirrors. A bottom mirror is stationary. A top mirror acts as the outputcoupler and is suspended by a flexible structure. The mirrors form aFabry-Perot filter such that the wavelength of tuned emission isproportional to the separation distance of the mirrors. Applying voltageacross actuator contact pads creates an electrostatic attractive forceat the MEMS actuator which pulls the top mirror down, thereby reducingthe cavity length and tuning a shorter wavelength of emission. FIG. 7Dshows static wavelength tuning of a MEMS-tunable VCSEL device obtainedby applying a DC voltage across the actuator. The attractive force,F_(a), is nonlinear in voltage, V, and deflection, δ, where g is theundeflected actuator gap distance, s is the permittivity, and A is thearea, as shown in Eq. 3.

$\begin{matrix}{F_{a} = \frac{V^{2}ɛ\; A}{\left( {g - \delta} \right)^{2}}} & {{Eq}.\mspace{14mu} 3}\end{matrix}$

The restoring force of the actuator, F_(s), is generally linearlyproportional to deflection, following the equation for a spring,F_(s)=k_(s)δ, where k_(s) is the spring constant of the actuator. At aparticular critical DC voltage and corresponding deflection, theelectrostatic attractive force exceeds the restoring force of the MEMSflexible structure and the actuator becomes unstable. A rapidacceleration of the actuator causes the top half of the actuator tocollide with the bottom part of the actuator, an event referred to as“pull-in” or “snap-down,” which is specifically avoided during normaloperation of a MEMS-tunable VCSEL. FIG. 7E shows the response of aMEMS-tunable VCSEL to a periodic voltage input signal. The dynamicresponse of the MEMS-tunable VCSEL wavelength tuning can bepreferentially controlled to produce wavelength sweep trajectories thatare optimized for a given application, as described in a US patentapplication, US 20140028997 A1, “Agile Imaging System,” herebyincorporated by reference.

The specific mechanism for changing the optical path length of the lasercavity in the VCL affects the wavelength tuning range and the wavelengthtuning dynamics. For example, a VCL in which the optical path length ofthe cavity is adjusted by changing the index of refraction of asemiconductor material will have a relatively small wavelength tuningrange because of limits in the change of the index of refraction of thematerial and the short gain material length, but will have the potentialfor extremely fast and flexible wavelength tuning dynamics. A VCL inwhich the optical path length of the cavity is adjusted by changing thespacing between the laser cavity mirrors with an electrostatic MEMSactuator will have moderate tuning range that is limited by snapdown andwill have fast and flexible wavelength tuning dynamics. A VCL in whichthe optical path length is adjusted by changing the spacing between thelaser cavity mirrors with a piezo-electric actuator will potentiallyhave a very long wavelength tuning range, but only moderately fastdynamics that will be limited by the relatively large mass of the movingcomponents. The specific mechanism for changing the optical path lengthof the laser cavity in a wavelength tunable VCL imposes limits on theupper bound of the wavelength tuning ability of the laser.

Different operating wavelengths require different gain material in thelaser cavity. Potential gain materials include, but are not limited to:InGaAs, AlInGaP, AlInGaAs, InGaAsP, InGaP, InP, AlGaAs, and GaAs. GaAsquantum wells would be used in about the 800-870 nm range, AlGaAs wellsin about the 730-800 nm range, AlInGaP and InGaP in about the 600-730 nmrange, and InGaAsP or AlInGaAs as alternative materials in about the800-900 nm range. InP can be used around 1310 nm and InGaAs can be usedaround 1050 nm. The specific gain material and processing of thematerial incorporated into a wavelength tunable VCL imposes limits onthe upper bound of the wavelength tuning ability of the laser.

A VCL can be optically pumped, as described in a paper, “OCT imaging upto 760 kHz axial scan rate using single-mode 1310 nm MEMS-tunable VCSELswith >100 nm tuning range” by V. Jayaraman, J. Jiang, H. Li, P. Heim, G.Cole, B. Potsaid, J. G. Fujimoto, A. Cable, CLEO:2011—Laser Appl. toPhotonic Appl., p. PDPB2, (2011). Optical pumping of a wavelengthtunable VCL can generate relatively wide wavelength tuning range, asdescribed in a paper, “High-sweep-rate 1310 nm MEMS-VCSEL with 150 nmcontinuous tuning range,” by V. Jayaraman, G. D. Cole, M. Robertson, A.Uddin, A. Cable, Electronics Letters, vol. 48, no. 14, pp. 867-869(2012). A VCL can also be electrically pumped, as described in a paper,“Wideband Electrically-Pumped 1050 nm MEMS-Tunable VCSEL for OphthalmicImaging,” by D. D. John, C. Burgner, B. Potsaid, M. Robertson, B. Lee,W. Choi, A. Cable, J. G. Fujimoto, and V. Jayaraman, LightwaveTechnology, Journal of, vol. no. 99, pp. 1. Because of the thickness ofintra-cavity current spreading layers, the tuning range of anelectrically pumped VCL can be limited because the free spectral rangeof the cavity is reduced. Consequently, the choice of pumping mechanismof a VCL can create design features that impose limits on the upperbound of the wavelength tuning ability of the laser.

The top mirror of the VCL laser cavity can be comprised of alternatinglow and high refractive index deposited materials, such as for exampleSiO2 and Ta2O5. Other deposited materials could be used as well,including but not limited to the list consisting of TiO2, HfO2, Nb2O5,Si, Ag, Al, Au, ZnS, ZnSe, CdF2, Al2F3, and CdS. For example, in thecase of a 10 period SiO2/Ta2O5 mirror having refractive indices of1.46/2.07 respectively, centered in a range of about 700 nm to about1600 nm, the theoretical lossless reflectivity can exceed about 99.5%over a range of at least 10% of the center wavelength, but the limit onthe usable high reflectivity range of the top mirror ultimately createsan upper bound on the wavelength tuning ability of the laser.

The bottom mirror of the VCL laser cavity can be comprised ofalternating quarter wave layers of GaAs and Aluminum oxide (AlxOy). TheGaAs/AlxOy mirror has a large reflectivity and wide bandwidth with asmall number of mirror periods. The preferred number of mirror periodsfor the back mirror, when light is coupled out the top mirror as shownin FIG. 7, is six or seven periods, creating a theoretical losslessreflectivity of >99.9%. Other implementations of this mirror could useAlGaAs/AlxOy, where the aluminum content of the AlGaAs is less thanabout 92%, so that it does not oxidize appreciably during lateraloxidation of the AlAs to form AlxOy. Use of AlGaAs instead of GaAs forthe low index material is advantageous for increasing the bandgap of thelow-index material to make it non-absorbing at the lasing wavelength orat the pump wavelength if the laser is optically pumped. Again, a limiton the usable high reflectivity range of the bottom mirror ultimatelycreates an upper bound on the wavelength tuning ability of the laser.

The output power of a VCL alone may not be sufficient for a givenapplication. An optical amplifier can be used to amplify the lightemission from the VCL to generate higher power wavelength emission.Common optical amplifiers suitable for amplifying the VCL output aresemiconductor optical amplifiers (SOA), booster optical amplifiers(BOA), doped fiber optical amplifiers and others. The gain performancevs. wavelength of an amplifier depends on the specific gain material,processing of the gain material, operating conditions of the gainmaterial, and pump conditions of the gain material. The gain materialand processing of the gain material incorporated into an amplifierimpose limits and an upper bound on the usable wavelength range of theamplifier.

When the VCL output emission is amplified by an optical amplifier, theoutput emission from the optical amplifier is a combination of amplifiedtuned emission and amplified spontaneous emission (ASE) from the gainmaterial in the amplifier. While the amplified tuned emission is narrowwavelength band and contributes to the useful signal of the instrument,the ASE introduces noise to the measurement. Further, in applicationswhere there are limits on the total exposure levels allowable on asample, as is the case for OCT imaging of humans, animals, and lightsensitive samples, the ASE counts towards the total exposure, but doesnot contribute useful signal. This effectively lowers the allowedexposure of tuned emission and degrades instrument sensitivity orperformance. Through proper design of the VCL and optical amplifiersystem, the ratio of ASE to tuned emission can be controlled torelatively small levels over wavelengths where there is sufficientoptical amplifier gain. However, over wavelengths where the gain of theoptical amplifier is low, the ratio of ASE to tuned emission canincrease, ultimately imposing limits and an upper bound on the usablewavelength range of the amplifier.

When the output emission of a VCL is amplified with an opticalamplifier, it can be advantageous to be able to adjust the gain of theoptical amplifier as a function of time or sweep wavelength. Forexample, a programmable current driver connected to a BOA can adjust thecurrent to the BOA to generate appropriate gain as a function ofwavelength or time to advantageously shape the output emission spectra.In OCT, the shape of the envelope of the OCT fringe can be made to beresemble an apodization window function (e.g. Hann, Hamming, Guassian,etc.) to reduce OCT point spread function sidelobes. In spectroscopy,the spectral output of the amplifier can be shaped to provide relativelyflat emission or emission shaped to emphasize certain wavelengths. Thecurrent driver can also be used to effectively turn the VCL emission onand off to block VCL emission from reaching the sample.

FIGS. 8A-8D show experimental data obtained from several VCL andamplifier components. FIG. 8A shows experimental data from an opticallypumped VCSEL source with a tuning range of approximately 1170 nm to 1265nm. FIG. 8B shows experimental data from an optically pumped VCSELsource with a tuning range of approximately 1240 nm to 1370 nm. There isan overlap of approximately 25 nm between these two VCSELs and together,they span approximately 200 nm. FIG. 8C shows experimental data from abooster optical amplifier (BOA) with gain from approximately 1180 nm to1280 nm. FIG. 8C shows experimental data from a BOA with gain fromapproximately 1220 nm to 1380 nm. These VCSELs and BOA can be cascadedor concatenated to achieve a larger wavelength tuning range than asingle device used alone.

FIG. 9A shows the frequency response of several different MEMS actuatordesigns experimentally tested for a MEMS-tunable VCSEL. By changing theactuator plate diameter attached to the moving top mirror and the widthand number of struts supporting the plate, different frequency responsesof the MEMS actuator can be obtained. For the designs shown, theactuator with a small plate diameter of 30 microns exhibits a large peakin the frequency response near the dominant mechanical resonantfrequency of the structure around 300 kHz. Increasing the plate diameterincreases the damping of the actuator, which broadens the resonant peakand allows the MEMS actuator to be driven at a wide range of sweepfrequencies and with customized waveforms to control the sweeptrajectory, as described in a US patent application, US 20140028997 A1,“Agile Imaging System”. However, when the MEMS-tunable VCSEL is drivenat frequencies away from the mechanical resonance, the actuator sweeptrajectory still exhibits oscillations at the resonant frequency.Further, higher order modes of mechanical resonance exist. For example,FIG. 9B shows results of a finite element analysis (FEA) of the 30 umplate design in which the 6th mechanical vibrational mode is shown withresonant frequency of 1.6 MHz. Other lower order modes exist (notshown), but the 6th mode shown here is of particular interest because itgenerates a change in the optical path length during resonance, whichcauses an associated change in wavelength trajectory at 1.6 MHz. As aconsequence of the dominant resonant mode and higher order modes thataffect the optical path length of the laser cavity, there is asweep-to-sweep variation when operating the MEMS-tunable VCSEL away fromthe mechanical resonance frequency. There is a tradeoff betweensweep-to-sweep stability and flexibility in generating difference sweeptrajectories in the MEMS actuator design. Increasing the resonant peak(or the quality factor or Q) of the MEMS actuator and operating theMEMS-tunable VCSEL at resonance decreases sweep-to-sweep variation, butat a cost of sweep trajectory flexibility. Decreasing the resonant peakof the MEMS actuator and operating the MEMS-tunable VCSEL away fromresonance increases the potential flexibility of the instrument tooperate at different sweep repetition rates, at different speeds, overdifferent sweep ranges, and over different sweep trajectories, but at acost of increased sweep-to-sweep variation. The sweep-to-sweep variationcreates a particular challenge when attempting to combine the sweeps ofmultiple wavelength swept VCL sources.

The VCL and more specifically the VCSEL is a unique light source withproperties that enable or improve instrument capability and performance.With a short cavity length on the order of several microns, the VCL canoffer fast and flexible tuning with a true single longitudinal lasermode. However, the sweep bandwidth for a given design is limited for thereasons described above related to limitations in laser gain material,mirror design, actuator performance, laser geometry, and amplifierperformance. Further, the sweep-to-sweep variation inherent in aMEMS-tunable VCSEL design that is optimized to operate at differentsweep repetition rates, at different speeds, over different sweepranges, and over different sweep trajectories exhibits significantsweep-to-sweep variation that generates uncertainty in the startingwavelength, wavenumber, or interferogram phase of each sweep. Thesweep-to-sweep variation of a MEMS-tunable VCSEL that has been optimizedfor low Q factor in order to support flexibility in sweep trajectory issignificantly more than the sweep-to-sweep variation for the non-VCLlaser technologies previously described. There is therefore both a needto use multiple swept light sources for applications that benefit froman increased spectral bandwidth and a need to effectively manage thesignificant sweep-to-sweep variation and sweep uncertainty inherent incertain wavelength swept VCL designs.

Generating Light from Multiple VCLs

FIGS. 10A-10D illustrate the basic concept of using two VCL lightsources in an instrument application. In FIG. 10A, light from VCL Source1 and light from VCL Source 2 is directed to a fiber coupler. The fibercoupler splits the light from each VCL source. A first portion of thelight from each VCL source is directed by the fiber coupler to aninstrument path and the other portion directed to an optional path formonitoring, diagnostics, and auxiliary functions. The monitoring,diagnostics, and auxiliary functions may include any one, anycombination, or all of: wavelength monitoring, power monitoring, opticaltrigger signal generation, optical k-clock generation, reference signalgeneration, and other monitoring, diagnostic, or auxiliary functions. Byturning VCL source 1 and VCL source 2 on and off with appropriatetiming, the wavelength sweeps from each VCL source can be interleaved,as shown in FIG. 10B. A portion of the sweep from VCL source 2 overlapsa portion of the sweep from VCL source 1, as shown in FIGS. 10B and 10C.FIG. 10C shows the sweep trajectories vs time (this plot shows the sweeptrajectory of the tuning mechanism, although light may or may not beemitted from the laser at any given time). A data acquisition system inthe instrument detects the light from the two sweeps and appropriatelycombines the two signals to generate a signal with extended wavelengthcontent. An illustrative example using an OCT instrument is shown inFIG. 10D. The OCT fringe generated from VCL source 1 is shown in FIG.10D (top). The OCT fringe generated from VLC source 2 is shown in FIG.10D (middle). In this example, there is overlap in spectrum between VCLsource 1 and VCL source 2 such that the OCT signals overlap inwavelength content towards the center of the fringe (indicated by thevertical line). A single combined OCT fringe, shown in FIG. 10D(bottom), can be generated by properly selecting and merging the datafrom the two individual OCT fringes. The combined data is properlyaligned at the boundary of the two individual fringes with respect towavelength, wavenumber, and interferogram phase. Further, the combinedfringe contains spectral data from both VCL source 1 and VCL source 2such that the wavelength span of the combined fringe is larger than thatof either VCL source 1 or VCL source 2 considered individually.

The optical power output from a VCL alone is not sufficient for manyapplications. FIGS. 11A-11D illustrate different configurations forcombining multiple VCLs with optical amplifiers to generate higheroutput power in the wavelength sweep. A single optical amplifier can beused in applications where the optical bandwidth of the opticalamplifier is wide enough to support the wavelength ranges of each of theindividual VLCs. An example embodiment using a single optical amplifiercomprises a 1050 nm swept source where the VCLs are eVCSELs with opticalbandwidths of approximately 60 nm and the BOA is a dual state designthat supports approximately 100 nm of optical bandwidth. The two VCLsand the one BOA can be configured as shown in FIG. 11A. Light from VCL 1and light from VCL 2 is directed to a fiber coupler. A portion of thelight from each VCL 1105, 1110 is directed by the fiber coupler to amonitoring, diagnostics, and auxiliary functions path. The other portionof the light is directed to an amplification path. The amplificationpath comprises an optical isolator 1115 and a booster optical amplifier(BOA) 1120. A polarization controller may also be used to align thepolarization state of the light entering the BOA with the BOA'spreferred polarization axis. Polarization maintaining fiber can also beused to control the polarization state. The coupling ratio of the fibercoupler can be selected according to the relative output powers of theindividual VCLs to provide an approximately equal output power of eachsweep to the instrument. Since the output power of VCL 1 and VCL 2 areoften similar, a coupling ratio of approximately 50:50 is most generallysuitable for this embodiment. While this example shows a BOA as theoptical amplifier, any suitable optical amplifier can be used in placeof, or in addition to a BOA. In general, a VCL source can comprise a VCLor can comprise a VCL and an optical amplifier. The VCL and opticalamplifier may or may not be integrated.

The optical bandwidth over which an optical amplifier has sufficientgain is often limited. One embodiment of the present invention comprisesmultiple optical amplifiers with different gain vs. wavelength response.An example embodiment using multiple optical amplifiers comprises twooptically pumped VCSELs with center wavelengths of approximately 1220 nmand 1310 nm and two BOAs with center wavelengths of approximately 1220nm and 1310 nm, as was shown in FIG. 8. The two VCLs 1125 and the twoBOAs 1130 can be combined as shown in FIG. 11B. Light from VCL1 isdirected to an optical isolator and amplified by BOA 1. Light from VCL 2is directed to an optical isolator and amplified by BOA 2. The outputsof BOA 1 and BOA 2 are directed to a fiber coupler. A portion of thelight from each of BOA 1 and BOA 2 is directed by the fiber coupler to amonitoring, diagnostics, and auxiliary functions path. The other portionof the light is directed to an instrument path. Other wavelength VCL andBOAs can be used in any of the different configurations.

The embodiments illustrated in FIG. 11A and FIG. 11B use a fiber couplerto combine the light from VCL 1 and VCL 2. The splitting ratio of thefiber coupler is chosen to provide approximately matched output power tothe instrument. Since VCL 1 and VCL 2 generally produce similar outputpower, the splitting ratio of the fiber coupler is generally chosen tobe approximately 50:50. The power requirements for the monitoring,diagnostics, and auxiliary functions are quite low, and in someapplications, a 50:50 coupler makes inefficient use of tuned emission.

FIG. 11C illustrates a single optical amplifier embodiment where lightfrom VCL 1 is directed to a fiber coupler with a splitting ratio of80:20. A 20% portion of the light is directed to a monitoring,diagnostics, and auxiliary function path. An 80% portion of the light isdirected to an optical switch. Light from VCL 2 is directed to a couplerwith a splitting ratio of 80:20. A 20% portion of the light is directedto a monitoring, diagnostics, and auxiliary function path. An 80%portion of the light is directed to an optical switch. The output of theoptical switch is directed to an amplification path comprising anoptical isolator and an optical amplifier. The optical switch selectsbetween the light from VCL 1 and VCL 2. Because of the low insertionloss of the optical switch, the combined losses from the 80:20 couplerand optical switch are less than the insertion loss of a 50:50 coupler.Other fiber coupler splitting ratios are possible with the goal ofmaximizing forward transmission from each VCL to the optical amplifierwhile supplying adequate power to the monitoring, diagnostics, andauxiliary function path. FIG. 11D illustrates an embodiment of thepresent invention comprising multiple optical amplifiers. Light from VCL1 is directed to a fiber coupler with splitting ratio of 90:10. A 10%portion of the light from VCL 1 is directed to a monitoring,diagnostics, and auxiliary function path. A 90% portion of the lightfrom VCL 1 is directed to an amplification path comprising an opticalisolator and BOA 1. Light from BOA 1 is directed to an optical switch.Light from VCL 2 is directed to a fiber coupler with splitting ration of90:10. A 10% portion of the light from VCL 2 is directed to amonitoring, diagnostics, and auxiliary function path. A 90% portion ofthe light from VCL 2 is directed to an amplification path comprising anoptical isolator and BOA 2. Light from BOA 2 is directed to an opticalswitch. The optical switch selects between the light from BOA 1 and BOA2. The embodiments illustrated in FIGS. 11C and 11D have a functionaladvantage over the embodiments illustrated in FIGS. 11A and 11B in thatboth VCL 1 and VCL 2 can be continuously generating light and do nothave to be turned on and off because the optical switch effectivelyblocks light from the deselected VCL source. The embodiments illustratedin FIGS. 11A and 11B have an advantage of not requiring an opticalswitch, which may improve reliability of the source. Although fibercouplers have been shown for the examples in FIG. 11, bulk opticscomponents, microfabricated components, fiber components, photonicintegrated circuit (PIC) devices, planar lightwave circuit (PLC)devices, and other beam splitting components can be suitably used.

FIG. 12 shows a schematic diagram of a practical implementation of thedual VCL swept source. A microcontroller (STMicroelectronicsSTM32F407IGT6) is connected to a 4 channel arbitrary waveform generation(AWG) chip (Analog Devices AD9106). A high voltage (HV) supply isconnected to adjustable DC bias generators, DC bias 1 and DC bias 2,which can be controlled by the microcontroller to generate aprogrammable DC output voltage. Channels 2 and 3 of the AWG chip areconnected to transformers through suitable circuitry to generate an ACcomponent of the drive signal to the MEMS actuators of eVCSEL 1 andeVCSEL 2. One end of each transformer is connected to the MEMS actuatorand the other end of the transformer is connected to the DC biasgenerator through a suitable circuit for each eVCSEL 1205, 1210respectively. Channel 1 of the AWG is connected to a programmablecurrent driver that controls the gain of the BOA 1215 to generatearbitrary gain profiles vs. time and can be used to turn the BOA on andoff in coordination with the sweep. Channel 4 of the AWG is connected toan eVCSEL selecting circuit. When the output voltage is zero, neither ofthe eVCSELs are energized. When the output of channel 4 is positiveabove a threshold voltage, then eVCSEL 1 is energized at constantcurrent. When the output of channel 4 is negative below a thresholdvoltage, then eVCSEL 2 is energized at a constant current. The output ofchannel 4 is rectified within the VCSEL select circuit to provide asweep trigger signal that is connected to the trigger input of thedigitizer subsystem. The sweep trigger can optionally have differentdurations to encode the sweeps so that the digitizer subsystem candistinguish data from eVCSEL 1 from eVCSEL 2. Light from eVCSEL 1 andeVCSEL 2 is split by a fiber coupler. A portion of the light from thefiber coupler is directed to an optical k-clock, wavelength monitoring,diagnostic, and reference signal generator. The other portion of lightis directed to an optical isolator and to the BOA. FIG. 12 shows onlyone example implementation of which other choices of chips, designs, andimplementations, and architectures are possible.

Challenges of Merging Multiple Detected Light Signals

The performance of an optical instrument that uses two or more sweptsources to increase the sweep range is generally very sensitive to thequality of the wavelength, wavenumber, or phase alignment at thejunction of the two constituent signals. As an example, FIGS. 13A-13Fshow the effects of wavelength (wavenumber, or phase) alignment betweentwo swept sources operation around 1050 nm. Equation 1 was used togenerate OCT fringes for a first swept source sweeping from 990 nm to1044 nm and a second swept source sweeping from 1041 nm to 1100 nm. Abackground component was added to the fringe to simulate the effects ofthe wavelength dependent splitting ratio in the fiber coupler before thebalanced detector of an OCT instrument. A fixed pattern reflection andthree sample reflections were simulated. The simulation also assumesthat optical k-clocking is implemented such that the A/D converterdigitizes at equal wavenumber (k) intervals. Since the k-clock generatorwas shared between the first and second swept sources, the wavelengths(or wavenumber) for which digitization takes place are the same over theregions of the spectrums where the two swept sources overlap. However,because of asynchronous clocks and timing between the FPGA, the trigger,and the optical k-clock, there is an at least one sample uncertainty inthe starting wavenumber of each acquisition. An uncertainty of onesample was assumed for the acquisition of the first swept laser and anuncertainty of one sample was assumed for the acquisition of the secondswept laser. A total of 300 OCT fringes were simulated with randomsample jitter of zero or one samples applied to each individual sweep.FIGS. 13A and 13B show the resulting OCT data from directly combiningthe two sweeps, where FIG. 13A shows a plot of all of the A-scans vsdepth in arbitrary units and FIG. 13B shows an OCT cross sectional imageor B-scan. The resulting image shows considerable broadband and highintensity artifacts in A-scans where there is phase mismatch between thetwo sweeps. Fixed pattern artifacts and a low frequency artifact arealso present where there is improper background subtraction. Animprovement to the image quality can be achieved by properly wavelength,wavenumber, or interferogram phase aligning the data from the secondsweep to the first sweep. FIG. 13C shows the resulting OCT data and FIG.13D shows the resulting OCT cross sectional image obtained afteradjusting the data in the second sweep by a one sample shift wherenecessary to properly align the phase of the sweeps. The broadband andhigh intensity artifact observed in FIG. 13B has been removed. However,low frequency artifacts and fixed pattern artifacts are still visible. Afinal step of adjusting the combined fringed to phase match thebackground sweep was performed to generate the OCT data shown in FIG.13E. As can be seen in FIG. 13E and FIG. 13F, the low frequencyartifacts and fixed pattern artifacts have been removed, revealing onlythe intended OCT data. Further insights into the importance of matchingthe phase between the first and second sweep can be gained from theresults shown in FIGS. 14A-14E, illustrating the effects of varying theposition at which the first and second sweep are joined. In FIGS.14A-14E, it is assumed that the first sweep is always phase aligned withthe background sweep data. A one sample starting wavenumber uncertaintyis simulated for the second sweep. In FIG. 14A, the position where thesweeps are joined occurs near the beginning of the sweep, as indicatedby the arrow in the top figure panel. Consequently, the resulting OCTdata is dominated by the one sample uncertainty in the startingwavenumber of the second sweep and the effect in the B-scan image shownin the bottom panel is very similar to that observed in standard oneswept source data without phase stabilization, as was illustrated inFIGS. 6C and 6D. As the position of joining the two sweeps is locatedprogressively further along the fringe, as illustrated in FIGS. 14B-14E,the type of artifact and visibility of the artifact changes accordingly.In the case of FIG. 14E, the majority of the OCT fringe is properlyaligned with only the tail end of the fringe with very small magnitudecontributing to the artifact. Consequently, the effect on the OCT dataand B-scan cross sectional image is minimal as this case most closelyrepresents properly phase stabilized data. The intermediate positions ofFIGS. 14B-14D show the most significant artifacts. With the position ofjoining the two sweeps at 3/10ths of the fringe length, FIG. 14B showslarge background subtraction artifacts and some broadband artifact fromthe phase discontinuity of joining the two sweeps. With the position ofjoining the two sweeps at ½ of the fringe length, FIG. 14C shows amixture of large broadband artifact from the phase discontinuity ofjoining the sweeps and background subtraction artifacts. With theposition of joining the sweeps at 7/10ths of the fringe length, FIG. 14Dshows large broadband artifact from the phase discontinuity of joiningthe two sweeps and a small artifact from improper backgroundsubtraction. In practice, an instrument using multiple swept sourceswould most likely comprise swept sources with approximately equal sweepranges, which results in the scenarios illustrated by FIGS. 14B-14D,which show high sensitivity to sweep alignment. A practical instrumentusing multiple swept sources must properly join the data from the two ormore sweeps with high precision to wavelength, wavenumber, and phasealignment. In general, the wavelength, wavenumber, or phase of the sweepis not detected by the instrument, preventing proper phase alignmentbetween the two or more sweeps. The present invention solves the problemof aligning the signal from two or more VCLs. The essential apparatusand methods that effectively combine the outputs of two or moreindividual lasers can also be adapted to phase stabilize the output ofinstrumentation using only a single laser.

Embodiments of the Present Invention

FIG. 15A shows a block diagram of an embodiment of the presentinvention. One embodiment of the present invention is an opticalinstrument comprising a first VCL source 1505 configured for generatingtuned emission over a first wavelength range to generate a firstwavelength sweep and a second VCL source 1510 configured for generatingtuned emission over a second wavelength range to generate a secondwavelength sweep. As shown in FIG. 15B, a portion of the tuned emissionfrom the first VCL (VCL Source 1) is directed to an optical system 1515and a sample 1520, while another portion of the tuned emission isdirected to a reference signal generator 1525. Similarly, as shown inFIG. 15C, a portion of the tuned emission from the second VCL (VCLSource 2) is directed to the optical system 1515 and a sample 1520,while another portion of the tuned emission is directed to the referencesignal generator 1525. There are many different ways to split andportion the light between these two light paths, which have beenpreviously described and will be described later in more detail. For thepurposes of differentiating the tuned emission that is directed to theoptical system and sample from the tuned emission that is directed tothe reference signal generator, the terms sample portion and referenceportion are used. Thus, an optical system delivers a sample portion ofthe first wavelength sweep and a sample portion of the second wavelengthsweep to the optical system and the sample. The exact value of thesample portion from the first wavelength sweep may or may not match theexact value of the sample portion from the second wavelength sweep.Similarly, the exact value of the reference portion from the firstwavelength sweep may or may not match the exact value of the referenceportion from the second wavelength sweep. Further, there may beadditional power splitting elements and optical elements that causepower loss such that the sample portion and reference portions ofemission do not exactly sum to the power output of the VCL source. Inthe context of the present invention, it is important that a least aportion of any one VCL source light emission be directed to an opticalsystem and at least a portion of the same VCL source light emission bedirected to a reference signal generator. The values and exact portionsdepend on the output powers of the VCL sources, the optical topography,and the requirements of the application. A reference signal generatorreceives at least a portion of the first wavelength sweep to generate areference signal for the first wavelength sweep and receives at least aportion of the second wavelength sweep to generate a reference signalfor the second wavelength sweep. A sample detector 1530 detects tunedemission from the first wavelength sweep that is affected by the sampleand tuned emission from the second wavelength sweep that is affected bythe sample and generates a sample signal for the first wavelength sweepand a sample signal for the second wavelength sweep, respectively. Adigitizer subsystem 1535 converts the sample signal from the firstwavelength sweep into sample digital data for the first wavelength sweepand converts the sample signal for the second wavelength sweep intosample digital data for the second wavelength sweep and converts thereference signal for the first wavelength sweep into reference digitaldata for the first wavelength sweep and converts the reference signalfor the second wavelength sweep into reference digital data for thesecond wavelength sweep. An alignment processor 1540 uses the referencedigital data for the first wavelength sweep and the reference digitaldata for the second wavelength sweep as input to process the sampledigital data for the first wavelength sweep and to process the sampledigital data for the second swept wavelength sweep to generate outputdigital data. The output digital data is aligned with respect to atleast one of: wavelength, wavenumber, and interferometric phase. Theoutput digital data contains at least a portion of the information inthe first wavelength sweep and at least a portion of the information inthe second wavelength sweep. In the context of an OCT instrument, theoutput digital data could represent a continuous interferogram spanninga wavelength range of the first VCL source and the second VCL sourcecombined. In the context of a spectroscopy system, the output digitaldata could represent absorption, reflection or emission vs. wavelengthin a scan of a sample with a wavelength spanning the range of the firstVCL source and the second VCL source combined. Light collection optics1545 may also be included in the apparatus or method. In the case ofOCT, the optical system may serve to direct light or tuned emission tothe sample and to collect light or tuned emission from the sample. Inthe case of spectroscopy, the optical system may serve to direct lightto the sample and a different light collection optics, called a samplelight collection optical system, may collect light from the sample, aswould especially be the case for transmitted light spectroscopy andcertain implementations of reflected light spectroscopy. Is it alsopossible that the optical system deliver light or tuned emission to thesample and also collect light or tuned emission from the sample, aswould be the case for certain implementations of reflected lightspectroscopy. In this way, light collection optics are not an essentialelement of all embodiments of the present invention. However, lightcollection optics are an element of certain embodiments of the presentinvention, as demonstrated with the example of transmitted lightspectroscopy. One embodiment of the present invention comprises the stepof collecting the first wavelength sweep affected by the sample and thesecond wavelength sweep affected by the sample.

This first example embodiment illustrates the present inventioncomprising a first VCL and a second VCL. Other embodiments of thepresent invention comprise a first VCL, a second VCL, and a third VCL. Amore general embodiment of the present invention comprises N VCLs.

In one embodiment of the present invention, at least one of the firstVCL source and the second VCL source comprises a VCSEL. In a morespecific embodiment of the present invention, at least one of the firstVCL source and the second VCL source comprises a MEMS-tunable VCSEL or apiezo-tunable VCSEL. In one embodiment of the present invention, atleast one of the first VCL source and the second VCL source comprises anoptical amplifier. In another embodiment of the present invention, atleast one of the first VCL source and the second VCL source produceswavelength sweeps with sweep-to-sweep variation. In another embodimentof the present invention, at least one of the first VCL source and thesecond VCL source is operable under different modes of operation,wherein the modes of operation differ in at least one of: sweeprepetition rate, sweep wavelength range, sweep center wavelength, andsweep trajectory. In one embodiment of the present invention, theoptical instrument further comprises an imaging interferometer, whereinthe imaging interferometer comprises a sample optical path, a referenceoptical path, and path interfering element, and wherein the opticalinstrument performs optical coherence tomography, and wherein the outputdigital data is further processed into A-scans.

The path interfering element could be a fiber coupler, wave guidecoupler, bulk optics beam splitter, or any other element that interfereslight from two different paths. In another embodiment of the presentinvention, the optical instrument further comprises a sample lightcollection optical system configured to collect a portion of tunedemission affected by the sample, and wherein the optical instrumentperforms spectroscopy. One possible suitable form of spectroscopy isFourier transform spectroscopy.

One embodiment of the present invention is a method for aligning digitaldata representing optical measurements from a sample comprising,generating a first wavelength sweep from the tuned emission of a firstVCL source and generating a second wavelength sweep from the tunedemission of a second VCL source. The method comprises directing a sampleportion of the first wavelength sweep and a sample portion of the secondwavelength sweep towards a sample to generate a first wavelength sweepaffected by the sample and a second wavelength sweep affected by thesample and collecting the first wavelength sweep affected by the sampleand the second wavelength sweep affected by the sample. The method alsocomprises detecting the first wavelength sweep affected by the sample togenerate a sample signal for the first wavelength sweep and detectingthe second wavelength sweep affected by the sample to generate a samplesignal for the second wavelength sweep. The method also comprisesdirecting a reference portion of the first wavelength sweep and thesecond wavelength sweep towards a reference signal generator. The methodcomprises generating a reference signal for the first wavelength sweepfrom the reference portion of first wavelength sweep and generating areference signal for the second wavelength sweep from the referenceportion of the second wavelength sweep. The method comprises convertingthe sample signal for the first wavelength sweep into sample digitaldata for the first sweep, converting the sample signal for the secondwavelength sweep into sample digital data for the second sweep,converting the reference signal for the first wavelength sweep intoreference digital data for the first sweep, and converting the referencesignal for the second wavelength sweep into reference digital data forthe second sweep. The method also computes a set of alignmentparameters, wherein the computing uses the reference digital data forthe first sweep and the reference digital data for the second sweep asinput, then generates output digital data representing the sample fromthe sample digital data for the first sweep and sample digital data forthe second sweep, wherein the output digital data is aligned withrespect to at least one of: wavelength, wavenumber, and interferometricphase, and wherein the output digital data is aligned using the set ofalignment parameters previously computed as input.

In one embodiment of the present invention, the method comprises tuningthe emission of at least one of the first VCL source and the second VCLsource with a MEMS actuator or a piezo actuator. In another embodimentof the present invention, the method comprises operating at least one ofthe first VCL source and the second VCL source under different modes ofoperation, wherein the modes of operation differ in at least one ofsweep repetition rate, sweep wavelength range, sweep center wavelength,and sweep trajectory. In one embodiment of the present invention, themethod comprises processing the output digital data into opticalcoherence tomography data. In another embodiment of the presentinvention, the method comprises processing the output digital data intospectroscopy data.

The present invention is not limited to a total number of two VCLsources. FIG. 15D shows N VCL sources directing light to the opticalsystem and reference signal generator of one embodiment of the presentinvention. One embodiment of the present invention is an opticalinstrument comprising a set of N VCL sources, the set of N VCL sourcesconfigured for generating tuned emission over N wavelength ranges togenerate N wavelength sweeps, where N is a number ranging from 2-6 andan optical system configured for delivering at least a portion of eachof the N wavelength sweeps to a sample and a reference signal generatorconfigured for receiving at least a portion of each of the N wavelengthsweeps to generate N reference signals and a sample detector configuredfor detecting tuned emission affected by the sample to generate N samplesignals and a digitizer subsystem configured for converting the N samplesignals from the N wavelength sweeps into sample digital data for the Nwavelength sweeps and converting the N reference signals for the Nwavelength sweeps into reference digital data for the N wavelengthsweeps and an alignment processor configured for using the referencedigital data for the N wavelength sweeps as input to process the sampledigital data for the N wavelength sweeps to generate output digitaldata, wherein the output digital data is aligned with respect towavelength, wavenumber, or interferometric phase.

One embodiment of the present invention is a method for aligning digitaldata representing optical signals from a sample generating N wavelengthsweeps from the tuned emission of N VCL sources, where N is a numberfrom 2-6; and directing at least a portion of the N wavelength sweepstowards a sample, wherein the tuned emission of the N wavelength sweepsis affected by the sample; and detecting the tuned emission of the Nwavelength sweeps affected by the sample to generate N sample signals;and directing at least a portion of the N wavelength sweeps towards areference signal generator; and generating N reference signals, one eachfor each of the N wavelength sweeps; and converting the N sample signalsinto sample digital data for the N wavelength sweeps; and converting theN reference signals into reference digital data for the N wavelengthsweeps; and computing a set of alignment parameters, wherein thecomputing uses the reference digital data for the N wavelength sweeps asinput; and generating output digital data representing the sample fromthe sample digital data for the N wavelength sweeps, wherein the outputdigital data is aligned using the set of alignment parameters previouslycomputed as input, and wherein the output digital data is aligned withrespect to at least one of: wavelength, wavenumber, and interferometricphase.

It is also possible to apply the apparatus and methods of the presentinvention to align multiple sweeps from a single VCL source or otherwavelength swept laser. FIG. 16A shows a block diagram of an embodimentof the present invention comprising a VCL source 1605 and FIG. 16B showsa block diagram of an embodiment of the present invention comprising awavelength swept source 1640. Also shown as arranged in each of theblock diagrams are: an optical system 1610, 1645; a sample 1615, 1650; areference signal generator 1620, 1655; a sample detector 1625, 1660; adigitizer subsystem 1630, 1665; an alignment processor 1635, 1670; andoptional light collection optics. Aligning multiple sweeps from the sameVCL source or other wavelength swept source with respect tointerferometric phase, wavelength, or wavenumber is important forapplications of OCT and spectroscopy that benefit from phase stabilizeddata.

Aligning Multiple Signals

The alignment processor takes as input the reference digital data forthe first wavelength sweep and the reference digital data for the secondwavelength sweep. The reference signal is generated from a referencesignal generator that creates an output in response to the wavelength orwavenumber of the incoming light. Details of the reference signalgenerator will be described later, but an example reference signal isshown in FIG. 17A (top). This example reference signal is morecomplicated than absolutely required, but it serves as a generic exampleof a filter that generates a reference signal with some degree ofcomplexity in the response to the wavelength of incoming light. In oneembodiment of the present invention, the reference signals for the firstand second sweeps are acquired with an optical k-clock and there isoverlap between the spectrums. In the region of overlapped spectrum, thesamples are acquired at the same wavelength or wavenumber, regardless ofthe sweep trajectory, due to the optical k-clock generating clocksignals at equal and repeatable wavenumber. In the presence ofdispersion in the k-clock interferometer, the spacing in wavenumber, k,can deviate from being equally space, but they are repeatable as afunction of wavelength or wavenumber. The task of aligning the signalsfrom the first and second sweeps can be accomplished with a correlationor matching search. FIG. 17A (top) shows an example reference signal asif acquired with a single wavelength sweep spanning the wavelength rangeof VCL1 and VCL2 combined. This reference signal spanning the combinedwavelength range represents the actual or ideal alignment of referencesignal data. However this reference signal is not generally available inan experimental apparatus that comprises two or more VCLs that aresweeping independently. Instead, a first reference signal for the firstwavelength sweep (FIG. 17A (middle)) and a second reference signal forthe second wavelength sweep (FIG. 17A (bottom)) are acquired withoverlapping samples where there is spectral overlap. Sweep-to-sweepvariation and trigger jitter create uncertainty in the proper alignment(number of samples of overlap) between the end of the first referencesignal and the start of the second reference signal. FIG. 17B (top)shows a first reference signal and multiple possible second referencesignals with −2, −1, 0, +1, and +2 samples of wavenumber alignmenterror. FIG. 17B (bottom) shows a zoomed in view on the region ofspectral overlap to highlight the −2, −1, 0, +1, and +2 samples ofwavenumber alignment error.

When there is an uncertainty in the temporal or spatial alignment ofdata from multiple sources, correlation techniques can be used toidentify the time, sample, or spatial correction that properly alignsthe data, called alignment parameters. Examples of methods to align datainclude autocorrelation, cross-correlation, difference calculations,similarity calculations and related techniques, all of which can be usedwith the present invention. The data may consist of an array or vectorof integer values, real values, binary values or other data storagetypes in memory. Alternately, in the case of searching for a rising orfalling edge transition, the alignment processor can count samples froma trigger signal that defines the start of acquisition until rising orfalling edges are encountered in the reference data associated with thefirst sweep, and count samples from a trigger until rising or fallingedges are encountered in the reference data associated with the secondsweep and use the indices of the rising or falling edges to define thewaveform. A correspondence match can be performed on this alternatestorage mechanism of the signal by calculating the differences in theindices for different offset values to find the best offset that matchesthe index values. Similar metrics, such as SSD, can be applied to findthe offset with the best match. Both the direct comparison of signalsand the comparison of counted values are considered part of acorrespondence match of the present invention. Other methods ofcomparing similarity of signals known in the art of signal processingare also included in the present invention. In one embodiment of thepresent invention, the range of uncertainty is known from thecharacteristics of the sweep-to-sweep variation and trigger jitter andthe proper offset to align the data, the alignment parameters, can bedetermined as follows.

A first set of reference digital data for the first wavelength sweep,{right arrow over (q)}₁, contains n₁ data points and a second set ofreference digital data for the second wavelength sweep, {right arrowover (q)}₂, contains n₂ data points. A subset of data or window of thedigital data consisting of l_(w) samples of the reference digital datafor the first sweep is used as a template signal, x_(t). A second subsetor window is extracted from the reference digital data for the secondsweep with an offset value, u, to form a comparison signal, x_(c)(u),also of length l_(w). A search can be performed to find the value of uthat most closely aligns the template signal to the comparison signal.The quality of the match between the template signal and the comparisonsignal is defined by a metric, ƒ(u), which is either minimized ormaximized with higher quality of match. Common metrics applicable to thecurrent invention include the sum of squared differences (SSD) andnormalized cross-correlation (NCC), among others.

The sum of squared differences is computed as:

${f_{SSD}(u)} = {\sum\limits_{i = 0}^{n - 1}{\left( {{x_{t}(i)} - {x_{c}\left( {i + u} \right)}} \right)^{2}.}}$

The normalized cross-correlation is computed as:

${{f_{NCC}(u)} = {\sum\limits_{i = 0}^{n - 1}\left( {{\overset{\sim}{x}}_{t}{{\overset{\sim}{x}}_{c}\left( {i + u} \right)}} \right)}},$where

{tilde over (x)}_(t)=(x_(t)−x _(t))/std(x_(t)) and {tilde over(x)}_(c)=(x_(c)−x _(c))/std(x_(c)), and where std( ) operator is thestandard deviation. The goal of the search is to find the offset value,u, that achieves the highest match between the template signal and thecomparison signal. The optimal value of u can be found by an exhaustivesearch or a numerical optimization acting over a range of offset values.The range of offset values is selected to include the worst case sampleuncertainty from sweep-to-sweep variation and trigger signal jitter.FIG. 17C shows the results of applying the search to the example data.FIG. 17C (top) shows the template signal and the comparison signal inthe left plot and the error signal obtained by subtracting the templatesignal from the comparison signal in the right plot. The offset value,the metric as calculated with the sum of squared differences, and themetric value as calculated with the normalized cross correlation arealso listed in the right column of the plots. Moving down the column ofplots in FIG. 17C, it can be seen that the value of the SSD decreasesand the value of the NCC increases with increasing offset value. At anoffset value of 10, the SSD value has reached a minimum value and theNCC has reached a maximum value as the comparison signal and thetemplate signal are properly aligned. Above an offset value of 10, theSSD value begins to increase and the NCC value decreases with increasingoffset value. FIG. 18A shows a plot of the SSD metric value and NCCmetric value vs. sample offset value. The offset value that properlyaligns the data corresponds to the minimum SSD value and the maximum NCCvalue, which occurs at an optical offset value, u*, of 10 sample points.

The digital data for the first wavelength sweep and the digital data forthe second wavelength sweep can be properly combined by selecting amerging point in the region of spectral overlap, copying or using thedata from the first sweep up to the merging point, and copying or usingthe data from the second sweep starting from the merging point, thenconcatenating the data. For example, with window length, l_(w),selecting the data signals, {right arrow over (r)}₁={right arrow over(q)}₁(1:(n₁−l_(w)/2)) and {right arrow over (r)}₂={right arrow over(q)}₂((u*+l_(w)/2):n₂), then concatenating the data into a combined dataarray, the properly aligned reference digital data can be generated as{right arrow over (r)} _(c)=[{right arrow over (r)} ₁ ,{right arrow over(r)} ₂].  Eq. 3

The results of the combined data array for this example are shown inFIG. 18B, which shows proper alignment and agreement with the idealsignal shown in FIG. 17A (top). Because the reference digital data andthe sample digital data are simultaneously clocked and at the samewavelength and wavenumber, the sample digital data can be obtained as{right arrow over (s)}₁={right arrow over (p)}₁(1:(n₁−l_(w)/2)) and{right arrow over (s)}₂={right arrow over (p)}₂((u*+l_(w)/2):n₂), thenconcatenating the data into a combined data array of properly alignedsample digital data as{right arrow over (s)} _(c)=[{right arrow over (s)} ₁ ,{right arrow over(s)} ₂],  Eq. 4

Where {right arrow over (p)}₁ and {right arrow over (p)}₂ are the sampledigital data for the first wavelength sweep and sample digital data forthe second wavelength sweep, respectively. In the case of searching fora rising or falling edge, u* can be determined from the indices foundfor the rising and falling edges.

The essential concept of matching signals using a correlation ormatching search with a template window and a comparison window can beused to align data in several different ways. FIG. 18C (top) shows afirst signal and FIG. 18C (bottom) shows a second signal in which thefirst and second signals have a region of overlap where they join. Atemplate window is extracted or read from the first signal and acomparison window is extracted or read from the second signal. Acorrelation or match search is performed to find the best offset for thecomparison window according to the selected metric. The best offsetvalue can be used to merge the second signal with the first signal togenerate a combined signal with proper wavelength, wavenumber, orinterferogram phase at the junction. The first and second signalsrepresent reference digital data for the first wavelength sweep andreference digital data for the second wavelength sweep in one embodimentof the present invention. FIG. 18D (top) shows a first signal that iscomplete and already representative of proper wavelength, wavenumber, orinterferogram phase alignment. FIG. 18D (middle) and FIG. 18D (bottom)show second and third signals for the data associated with the first andsecond halves of the complete signal shown in FIG. 18D (top), with aregion of overlap where the two signals meet. A template window isextracted or read from the first signal. A comparison window isextracted or read from the second signal and the results of thecorrelation or match search used to align the second signal with thefirst signal. A comparison window is extracted or read from the thirdsignal and the results of the correlation or match search used to alignthe third signal with the first signal. Because the second and thirdsignals are now aligned to the first signal, the second and thirdsignals are now also aligned to each other and a complete signal can becreated from the second and third signals. The first signal could be theresult of merging two reference signals, as would be the result ofapplying the approach shown in FIG. 18C. The second signal couldrepresent the reference digital data for the first wavelength sweep andthe third signal could represent reference digital data for the secondwavelength sweep that needs to be combined. The correspondence match canbe used to properly combine two sweeps from two different VCL sources toproduce a phase aligned OCT interferogram or spectroscopy measurement,for example. Applied in this way, the correspondence match also phasestabilizes multiple consecutive sweeps from the same VCL source to thefirst signal. The correspondence match can properly join two sweeps fromdifferent VCL sources and it can also be used to phase stabilizemultiple consecutive sweeps to generate phase stabilized output digitaldata.

In one embodiment of the present invention, the alignment processorcomputes a correspondence match between a subset of data from thereference digital data for the first wavelength sweep and a subset ofdata from the reference digital data for the second wavelength sweep orbetween a subset of data derived from the reference digital data for thefirst wavelength sweep and a subset of data derived from the referencedigital data for the second wavelength sweep as part of the processingto generate output digital data. Data derived from the reference digitaldata is data from the A/D converter that has been further processed. Thefurther processing may include subselection of data, high passfiltering, low pass filtering, or any other mathematical processing ofthe data performed before the correspondence match.

The advantages of phase stabilizing data have been previous described.An embodiment of the present invention may generate a first sweep from afirst VCL source, s_(t1) ^(v1), with associated reference digital data,r_(t1) ^(v1), and a first sweep from a second VCL source, s_(t1) ^(v2),with associated reference digital data, r_(t1) ^(v2). The embodiment maythen generate a second sweep from the same first VCL source, s_(t2)^(v1), with associated reference digital data, r_(t2) ^(v1), and asecond sweep from the same second VCL source, s_(t2) ^(v2), withassociated reference digital data, r_(t2) ^(v2). A correspondence matchcan be performed between r_(t1) ^(v1) and r_(t1) ^(v2) to generate acombined sweep and associated output digital data, d₁. A correspondencematch can be performed between r_(t2) ^(v1) and r_(t2) ^(v2) to generatea combined sweep and associated output digital data, d₂. At this point,d₁ and d₂ are wavelength, wavenumber, or interferometric phase alignedwithin their own respective output digital data set. However, d₁ and d₂may not be phase stabilized relative to each other. An additionalcorrespondence match can be performed between r_(t1) ^(v1) and r_(t2)^(v1) to determine the relative wavelength, wavenumber, orinterferometric phase between the two sweeps. The output digital data,d₂, can then be adjusted to phase align d₂ to d₁ using the same methodsof sample shifting or interpolating as described for the case of acombining and wavelength correcting the wavelength, wavenumber, orinterferometric phase between a first VCL source and a second VCLsource. Subsequent sets of output digital data, as would compose a largeOCT data set, can be similarly aligned to d₂ in order to generate acomplete collection of output digital data sets that are all mutuallywavelength, wavenumber, or interferometrically phase aligned, as isdesirable for reducing fixed pattern noise in OCT images, for example.In one embodiment of the present invention, the instrument generates afirst output digital data and a second output digital data, wherein thefirst output digital data is aligned to the second output digital datato phase stabilize the second output digital data to the first outputdigital data.

One embodiment of the present invention is a method comprising repeatingthe steps to generate a first output digital data and a second outputdigital data and aligning the second output digital data to the firstoutput digital data to generate a set of phase stabilized output digitaldata.

An embodiment of the present invention comprises a reference signalgenerator. Different reference signal generators can be used in thecurrent invention, as illustrated in FIG. 19. In FIG. 19A, the referencesignal generator comprises a Fabry-Perot filter or etalon 1905 and adetector 1910. A Fabry-Perot filter comprises two parallel reflectivesurfaces. An etalon comprises an optical substrate with two parallelsurfaces that are reflective. The operating principles of a Fabry-Perotfilter and an etalon are similar and for the purposes of the discussionof this present patent, can be used interchangeably. The transmission,T, of a Fabry-Perot filter or etalon is a function of wavelength, λ, andcan be tuned by adjusting the mirror reflectivity, R, index ofrefraction, n, spacing between the mirrors, l, and the angle ofincidence of the incoming beam, θ, according to:

$\begin{matrix}{{{T(\lambda)} = \frac{\left( {1 - R} \right)^{2}}{1 + R^{2} - {2R\mspace{11mu}{\cos(\delta)}}}},{{{where}\mspace{14mu}\delta} = {\left( \frac{2\pi}{\lambda} \right)2{nl}\mspace{11mu}{{\cos(\theta)}.}}}} & {{Eq}.\mspace{14mu} 5}\end{matrix}$

Noticing that the term,

$\frac{2\pi}{\lambda},$is proportional to the wavenumber, k, it can be seen that the resultingtransmission is periodic in wavenumber such that when the transmissionis sampled at equal k intervals, as is achieved with optical k-clocking,the result is a series of periodic transmission peaks, as shown in FIG.19B. As will be described later, the position of the transmission peakscan be used to properly phase align the OCT fringe data. One embodimentof the present invention comprises a reference Fabry-Perot filter oretalon and a reference detector, wherein the reference Fabry-Perotfilter or etalon is configured to filter tuned emission and wherein thefiltered tuned emission is directed to the reference detector togenerate the reference signals in the reference signal generator.

An alternate embodiment of the present invention uses a reference signalgenerator comprising an interferometer 1915 and detector 1920, as shownin FIG. 19C. Many different interferometer topologies are possible,including Mach-Zehnder, Michelson, common path, and associated variants.In general, the resulting fringe phase and amplitude is a function ofthe wavelength, such as that described by Eq. 1, and can be tuned byadjusting the effective fringe depth, (z_(r)−z_(s)), where

$z_{r} = {{\frac{l_{1}}{2}\mspace{14mu}{and}\mspace{14mu} z_{s}} = \frac{l_{2}}{2}}$to account for the single pass instead of double pass of light in theMach-Zehnder interferometer, where l₁ is the path length of a firstMach-Zehnder arm and l₂ is the path length of the second Mach-Zehnderarm. The resulting reference fringe is shown in FIG. 19D, which has thecharacteristic of linear phase evolution because the optical k-clockingsamples at equal k intervals. As will be described later, positions ofthe peaks and valleys or the zero crossings in the reference fringe canbe used to properly phase align the OCT fringe data. One embodiment ofthe present invention comprises a reference interferometer and areference detector, wherein the reference interferometer is configuredto interfere tuned emission and wherein the interfered tuned emission isdirected to the reference detector to generate the reference signals inthe reference signal generator.

Another alternate embodiment of the present invention uses a referencesignal generator comprising a fiber Bragg grating (FBG) 1925 anddetector 1930, as shown in FIG. 19E. The fiber Bragg grating has hightransmission for most wavelengths and high reflection at a particulardesign wavelength. The resulting signal as the laser sweeps wavelengthsis shown in FIG. 19F and consists of a region of high signal over thewavelength region where the FBG has high transmission with a sharpvalley in the signal where the FBG has high reflection, followed againby a high signal over the remaining wavelengths of the sweep. As will bedescribed later, the position of the valley in the reference signal canbe used to properly phase align the OCT fringe data. It is also possibleto use an FBG in reflection. An FBG combined with an optical coupler oran optical circulator can generate a reflected signal at the wavelengthof the FBG that can be detected with a detector, as is commonlypracticed. Other optical devices can also generate a signal at aspecific or repeatable wavelength, such as a grating and diode detectorwhere the beam translates over the diode detector as a function ofwavelength. Bragg gratings can also be implemented in forms other thanfiber Bragg gratings, such as in glass substrates, photonic integratedcircuits (PICs), or planar lightwave circuits (PLCs). A narrow notch orbandpass filter can also generate a signal at a specific wavelength. Oneembodiment of the present invention comprises a reference Bragg gratingor a reference fiber Bragg grating and a reference detector, wherein thereference Bragg grating or reference fiber Bragg grating is configuredto filter tuned emission and wherein the filtered tuned emission isdirected to the reference detector to generate the reference signals inthe reference signal generator. One embodiment of the present inventioncomprises a reference notch filter, reference bandpass filter, referencediffraction grating, or reference prism and a reference detector,wherein the reference notch filter, reference bandpass filter, referencediffraction grating or reference prism is configured to filter tunedemission and wherein the filtered tuned emission is directed to thereference detector (1930) to generate the reference signals in thereference signal generator.

Yet another alternate embodiment of the present invention comprises areference signal generator comprising a mirror 1935 with reflectivitythat changes as a function of wavelength and two detectors, as shown inFIG. 19G. Light enters the reference signal generator and is directed tothe mirror. The reflectivity of the mirror changes with wavelength to beeither monotonically increasing or monotonically decreasing over awavelength range of interest. Two examples of such a mirror design arespecified in Table 1 with the reflectivity of the mirrors shown in FIG.20A (top). Design 1 is the wide bandwidth filter and design 2 is thesteep slope filter. As determined by the reflectivity of the mirror at aparticular wavelength, a portion of the light is reflected from themirror and directed to a first detector, A, and the other portion of thelight transmits through the mirror and is directed to a second detector,B. The difference between the signal from detector A and detector B iscalculated and normalized by the sum of the signals from detector A anddetector B. The calculation of the difference in the detector signalscan be accomplished using an analog circuit comprising an operationalamplifier used in a difference calculation configuration. Thecalculation of the sum of the signals from detector A and detector B canbe accomplished using an analog circuit comprising an operationalamplifier used in a summing configuration. The division of the (A−B)signal by the (A+B) signal can be accomplished by using a four quadrantmultiplier, such as the Analog Devices AD835 chip, or circuitscomprising log amplifiers, difference amplifiers, and an antilogamplifier. The calculation can also be performed digitally with each ofsignals A and B being acquired with an analog to digital converter andthe math operations performed in hardware or software. FIG. 19H showsthe signal vs. wavelength for detector A and detector B. The sensoritself outputs a signal, S. Because the sensor signal is normalized bythe total signal, the sensor output is a function of wavelength andindependent of input power. A lookup table and interpolation can be usedto convert the sensor signal S to wavelength as λ=ƒ(S). FIG. 19I showsand example of the decoded wavelength as a function of A/D samplenumber, calculated as:

$\begin{matrix}{S = \frac{\left( {A - B} \right)}{\left( {A + B} \right)}} & {{Eq}{.6}}\end{matrix}$

TABLE 1 1050 nm Filter Designs Index of Thickness (nm) Thickness (nm)Layer Material Refraction Design 1 Design 2 1 Air 2 Ta2O5 2.12404 91.607124.78 3 SiO2 1.489952 139.216 186.37 4 Ta2O5 2.12404 103.759 132.82 5SiO2 1.489952 153.488 194.69 6 Ta2O5 2.12404 109.677 139.29 7 SiO21.489952 158.247 208.05 8 Ta2O5 2.12404 110.569 138.04 9 SiO2 1.489952155.592 209.22 10 Ta2O5 2.12404 102.489 143.69 11 SiO2 1.489952 126.076206.60 12 Ta2O5 2.12404 83.716 157.57 13 SiO2 1.489952 138.748 212.59 14Ta2O5 2.12404 104.24 140.22 15 SiO2 1.489952 116.253 178.04 16 Ta2O52.12404 53.798 119.74 17 Glass Substrate

Different filters can be designed at 850 nm, 1050 nm, 1310 nm, 1550 nm,or any other wavelength required as in known in the art of filterdesign. The filter and apparatus as described acts as a referencewavemeter. Other wavemeter implementations are possible. One embodimentof the present invention comprises a reference wavelength meter andreference detectors, wherein the reference wavelength meter receivestuned emission and the reference detectors is configured to generate thereference signals as a function of tuned emission wavelength in thereference signal generator.

An embodiment of the present invention can use any one of many differentreference signal generators. The signal from the reference generatorencodes the absolute or relative phase, wavelength, or wavenumber of thesweep in such a way that the instrument signal data obtained withmultiple sweeps can be properly combined with phase, wavenumber, orwavelength matching between sweeps. One embodiment of the presentinvention is a method that comprises directing a reference portion ofthe first wavelength sweep and the second wavelength sweep through atleast one of: a Fabry-Perot filter, an interferometer, a Bragg grating,a fiber Bragg grating, a reference notch or bandpass filter, adiffraction grating, a prism, a filter, and wavelength meter in thereference signal generator. Another embodiment of the present inventioncomprises at least one of: a Fabry-Perot filter, an interferometer, aBragg grating, a fiber Bragg grating, a reference notch filter, adiffraction grating, a prism, a filter, an etalon, and wavelength meterin the reference signal generator configured for generating the Nreference signals.

More specific embodiments of the present invention are described asfollows. The discussion starts with a description of an embodiment usingtwo channels of acquisition with an optical k-clock. Note, however, thatmany of the fundamental concepts taught in the context of the twochannel embodiment using an optical k-clock extend to embodiments withdifferent numbers of channels and with internal clocking whereappropriate, including high pass filtering and the specifications andmethods related to the various reference signal generators described andprocessing of signals thereof.

Two Channel Acquisition with Optical k-Clock

FIG. 21 shows a schematic diagram of an OCT system that uses twochannels of data acquisition and an optical k-clock. In practice, theoptical k-clock may be external to the multi-VCSEL source or part of thesame unit, as would likely be the case for an OEM product. Oneembodiment of the present invention is a method comprising the step ofconverting the sample signal for the first wavelength sweep into sampledigital data for the first sweep with substantially equal wavenumberspacing between sample points. Light from the multi-laser swept source2105 is divided by a first fiber coupler 2110. A majority portion of thelight is directed to an OCT interferometer 2120 while the other portionof light is directed to a second fiber coupler 2115. A portion of thelight from the second fiber coupler is directed to a reference signalgenerator 2130 and the other portion is directed to an optical k-clocksystem 2135. The splitting ratios of the fiber couplers are chosen tomaximize power to the OCT system while still supplying enough power tothe reference signal generator and the k-clock for functionality. Avalue of approximately 80:20 to 90:10 for the first coupler and 50:50for the second coupler would be typical. The exact choice of couplersplitting ratio depends on the specific OCT imaging application. The twochannels of the A/D converter sample simultaneously with acquisition ofdata occurring on rising or falling or both rising and fallingtransitions of the electrical k-clock signal. Channel 1 of the A/Dconverter samples data from the OCT detector. Channel 2 of the A/Dconverter samples data from the reference signal generator. Anelectrical line trigger synchronization signal from the multi-laserswept source initiates acquisition of the digitizer subsystem 2140 on arising or falling edge transition and is approximately aligned in timewith the start of the sweep of the first laser. The digitizer subsystemacquires a pre-determined number of samples sufficient to capture theOCT interferogram from the first swept laser. A second electrical linetrigger rising or falling edge transition is approximately aligned intime with the start of the sweep of the second laser. The digitizersubsystem acquires a pre-determined number of samples sufficient tocapture the OCT fringe from the second swept laser. The datasimultaneously obtained from the reference signal generator is used toproperly align and combine the fringe data from the first sweep and thefringe data from the second sweep to generate a combined data set thatspans the wavelength range of the first and second lasers and iscontinuous and properly aligned with respect to wavelength, wavenumber,or interferogram phase.

One embodiment of the present invention is an OCT instrument comprisinga Fabry-Perot filter in the reference signal generator, as shown in FIG.19A. The OCT instrument further comprises an optical k-clock generator,as shown in FIG. 21.

The function of one embodiment of the present invention is illustratedwith an example imaging scenario. An OCT sample that is a single mirrorreflection generates OCT fringes for a first sweep, labeled “Ch 1signal” and “sweep 1” in FIG. 22A (top) and a second sweep, labeled “Ch1” and “sweep 2” in FIG. 22A (top). Both of these signals are detectedby channel 1 of the digitization system. In practice, the sample wouldnot be a mirror, but an object or specimen to be imaged or measured. Asecond channel, channel 2, of the digitizer subsystem simultaneouslysamples the signal from the Fabry-Perot filter to generate the signalslabeled “Ch 2” and “sweep 1” for the first sweep and “Ch2” and “sweep 2”for the second sweep in FIG. 22A (bottom). In this simulation, theoptical path length of the Fabry-Perot filter is 105 microns and thereflectivity is 0.5 for each mirror. The first sweep spans thewavelength range of 990 nm-1044 nm and the second sweep spans thewavelength range of 1041 nm-1100 nm, so there is 3 nm of overlap betweenthe two sweeps that is detected in both the OCT fringe and theFabry-Perot signals. Because of possible sweep-to-sweep variation in theVCL and uncertainty in the starting wavelength (or wavenumber) of thesweep due to asynchronous clocks between the optical k-clock generatorand the digitization system, the starting wavelength (or wavenumber) ofthe sweep data that is acquired cannot be known and the digitized datasuffers from jitter. However, the effects of sweep-to-sweep variationand asynchronous clock jitter are bounded and in practice result in onlya few samples of starting wavelength (or wavenumber) uncertainty. Theabsolute number of sample jitter is usually between −1 to 1 or −50 to 50samples, depending on the specific VCL design, data acquisition design,and operating conditions. It is therefore necessary to determine thesample shift that properly aligns the second sweep with the first sweep.Because the wavelength and wavenumber of the OCT sweep and theFabry-Perot signal are inherently coupled by the synchronous sampling ofthe two channels of the A/D converter, it is possible to determine theappropriate shift in the Fabry-Perot signal (or other reference signalgenerator) and apply the same shift to the OCT signal data to achieveproper data alignment. A search and correspondence match can be appliedto the Fabry-Perot data, as shown in FIG. 22B. In this example, theoverlap between the two sweeps is large and the sample jitter is assumedto be less than 50 samples, setting the size of the search that will berequired. A reference signal consisting of a 20 sample window extractedfrom the end of the first sweep is used as a template for matching isshown in the top row of FIG. 22B. A comparison signal consisting of a 20sample windows extracted from the start of the second sweep is used forcomparison to the template. The starting sample of the comparison signalis determined by an offset value defining the first sample of thecomparison window. This offset value is the alignment parameter thatmust be computed for the purposes of properly aligning the data. Thealignment parameters are generally offset values that define properalignment of the data with respect to phase, wavelength or wavenumber.In this example the alignment parameter is an integer value defining theproper offset. The alignment parameters can also be fractional or real,as will be illustrated in later examples and the number of alignmentparameters depends on the specific correction method.

A metric is defined to quantify the quality of the match such that thevalue of the metric decreases in value with improvement in the closenessof match. In this example embodiment of the present invention, the sumof squared differences (SSD) between the reference signal and thecomparison signal is used as the metric. FIG. 22B shows the result ofdifferent offset values on the reference signal, the comparison signal,and the metric value using the sum of squared differences. The propershift to align the two fringes is 41 samples. At an offset of 32 samples(left column of FIG. 22B), the Fabry-Perot transmission peak in thereference signal occurs before the Fabry-Perot peak in the comparisonsignal. The resulting difference signal shows a large error between thetwo input signals and the metric as calculate has a value of 5.36. At anoffset of 41 samples (middle column of FIG. 22B), the reference signaland the comparison signal are aligned, resulting in no error and ametric value of 0. At an offset of 45 samples, the reference signaloccurs after the comparison signal, resulting in an error in thedifference signal and a metric value of 1.31. FIG. 22C shows a plot ofthe metric value vs. offset value. The proper offset can be determinedby selecting the offset that corresponds to the minimum value of themetric function. FIG. 22D shows a plot of the OCT fringe with the firstsweep plotted with an “x” marker and the second sweep plotted with an“o” marker where the second sweep has been offset by 41 samples. The topplot of FIG. 22D shows the entire OCT fringe and the bottom plot shows azoom on the centermost samples. The samples in the OCT fringe betweenthe first and second sweeps are perfectly aligned and a combined sweepcan be constructed by selecting a junction sample and including thefirst sweep up to the sample before the junction sample and starting thesecond sweep at the junction sample. The junction sample can be chosento be any sample where there is overlap between the first and secondsweep, but would preferably be selected near the center of the region ofsample overlap. Averaging of the data in the overlapped region is alsopossible. In this example, the method of Eq. 4 is used to join the twofringes. FIG. 22E confirms the effectiveness of the approach by plottingthe fringe (top row) and Fast Fourier Transform (FFT) of the fringe(bottom row) for the case of simply concatenating the two sweeps withoutregard to phase alignment (left column) and properly phase aligning thedata according to the approach described by Eq. 3 (right column). In thecase of simply concatenating the sweeps, there is a phase discontinuityand the resulting PSF after Fourier transformation shows a degraded OCTaxial point spread function with large sidelobes and broadbandartifacts. In the case of the properly phase combined data, theresulting point spread function is transform limited and identical tothe best PSF that can be obtained for this data.

The same method of correspondence matching is effective for otherembodiments of the present invention using a reference signal generatorcomprising an interferometer, fiber Bragg grating, notch or bandpassfilter, or wavelength meter or other. In all cases described, thecorrespondence search identifies the proper offset required to align thefirst and second sweeps of the laser.

For the embodiment of the present invention comprising a wavelengthmeter, the transmission response of the wavelength dependent filteraffects the robustness of the approach to noise. FIG. 20A (top) showsthe reflectivity vs. wavelength for a first dielectric mirror design,labeled “Wide Bandwidth Filter” with design specified in Table 1 asDesign 1 and a second dielectric mirror design, labeled “Steep SlopeFilter” with design specified in Table 1 as Design 2. The sensor outputof the two filters as calculated using Eq. 6 is shown in FIG. 20A(bottom). The “Steep Slope Filter” design has been optimized to providea steep slope in the reflectivity vs. wavelength around the wavelengthwhere the two sweeps overlap. The steeper slope increases the change inthe difference signal, making the embodiment using the Steep SlopeFilter more resistant to noise. However, while the Wide Bandwidth Filtercan be used to determine the wavelength of the sweep over the entiresweep range of both laser combined, the Steep Slope Filter can only beused near the wavelength region where the two sweeps combine because ofambiguities introduced by the non-monotonicity of the signal. Using theSteep Slope Filter, the OCT fringes for the first and second sweeps areshown in FIG. 20B (top) and the wavelength meter sensor signal is shownin FIG. 20B (bottom). The improvement in the amount of change in thedifference signal can be seen by comparing the results of the WideBandwidth Filter, shown in FIG. 20C, and the Steep Slope Filter, shownin FIG. 20D. The difference in metric function value as calculated withthe SSD are larger for the Steep Slope Filter than for the WideBandwidth Filter, making the Steep Slope Filter approach more robust tonoise.

FIG. 23A shows an embodiment of the present invention comprising a firstand a second etalon or Fabry-Perot filter 2305, 2310 with different pathlengths and a first and a second detector 2315, 2320, each respectivelyassociated with a corresponding etalon or Fabry-Perot filter 2305, 2310.The analog outputs of the detectors are summed by an electrical summingcircuit 2325. FIG. 23B shows the electrically summed signal, which canbe acquired by a second channel of an A/D converter that issimultaneously sampled with the sample data. In the case of opticalk-clocking, differences in sweep velocity are automatically accommodatedand the resulting reference signal can repeat (as would be the case withan reference MZI and Fabry-Perot filter), causing potential ambiguity inalignment. An advantage to the embodiment shown in FIG. 23A is that thereference signal is uniquely associated with and changes with thedifferent portions of wavelength sweep to remove that potentialambiguity.

FIG. 24A shows a schematic diagram of a reference signal generatorcomprising two etalons or Fabry-Perot filters. A first reference etalonor Fabry-Perot filter is of a different length than a second etalon. Theoptical signal from the first etalon or Fabry-Perot filter is detectedby a first detector. The optical signal from the second etalon orFabry-Perot filter is detected by a second detector. Each detectorconverts the optical signal from the etalon into an electrical signal.The analog outputs from the first reference detector and the secondreference detector are directed to a first comparator and a secondcomparator, respectively. The comparators compare the analog signal fromthe detector to a threshold voltage and output a digital output when theanalog voltage is above the threshold voltage. The comparator may havehysteresis to help reduce the effects of noise. The digital outputs fromthe first and second comparators are directed to a logic OR gate orlogic OR circuit 2405. The logic OR gate outputs a digital high signalwhen either of the inputs to the logic OR gate or circuit are high.Variations of the logic OR gate or logic, such as exclusive OR (XOR),NOR, XNOR, and others are also possible and included in the presentinvention. Note that the electrically summed signal from FIG. 23B couldalso be converted to a digital signal through thresholding and acquiredwith a digital input. The etalons or Fabry-Perot filters may be fibercoupled. The etalons or Fabry-Perot filters can be constructed ofbulk-optics or be equivalents in a PIC or PLC. In one embodiment of thepresent invention, the etalons or Fabry-Perot filters are thin plates ofglass. The thin plates of glass are coating on both sides withreflective coatings. The thin plates of glass are placed in front ofphotodetectors to receive collimated light beams with optional lensesand fiber delivery to the photodetector. One embodiment of the presentinvention comprises a first etalon or Fabry-Perot filter configured tofilter tuned emission and a second etalon or Fabry-Perot filterconfigured to filter tuned emission and is of a different optical pathlength than the first etalon or Fabry-Perot filter and first referencedetector configured to receive filtered tuned emission from the firstetalon or Fabry-Perot filter and a second reference detector configuredto receive filtered tune emission from the second etalon or Fabry-Perotfilter, wherein the signals from the first and second referencedetectors are combined with a summing circuit or a logic OR circuit togenerate the reference signals in the reference signal generator.Another embodiment of the present invention comprises a first etalon orFabry-Perot filter configured to filter tuned emission and a secondetalon or Fabry-Perot filter configured to filter tuned emission and isof a different optical path length than the first etalon or Fabry-Perotfilter and a reference detector, wherein the filtered tuned emissionfrom both the first and the second etalons or Fabry-Perot filters aredirected to an active area of the reference detector to generate thereference signals in the reference signal generator.

Consider a single VCL source directing light into the reference signalgenerator shown in FIG. 24A. The first etalon has an optical path lengthof 197 microns and the second etalon has an optical path length of 200microns. All surfaces of the etalon are coated with a dielectric coatingto achieve a reflectivity of 0.9 over the spectral range of at least1000 nm to 1100 nm wavelength. FIG. 24B (top) shows the optical signalas filtered by the first and second etalons, etalon 1 and etalon 2,respectively. A threshold voltage of 0.1 of the full optical scale ischosen, as indicated by the black horizontal line in FIG. 24B (top). Ifthe optical signal is above the threshold voltage, the respectivecomparator will output a high digital output voltage. If the opticalsignal is below the threshold voltage, the respective comparator willoutput a low digital voltage. The comparators may optionally containcircuitry to support hysteresis capability. The output signals from thecomparators are shown in FIG. 24B (middle) for the first and secondetalons, etalon 1 and etalon 2, respectively. The outputs, of thecomparators are directed to the input of the logic OR gate, whichoutputs a digital high signal when either or both of the inputs arehigh, as shown in FIG. 24B (bottom). The signal coming from the logic ORgate has the advantages of encoding the direction of the optical sweepand the local wavelength of the optical sweep because the local spacingof the peaks from the first and second etalons changes with changingwavelength. The reference signal generators shown in FIGS. 23A and 24Acan be used with one, two, or more VCL sources or wavelength sweptsources.

FIGS. 25A-25F show the signals obtained by an embodiment of the presentinvention that comprises two etalons of different length and a first anda second VCL, which generate a first and second sweep, respectively.FIG. 25A shows the signals detected by the first and second detectorsfor the first sweep and FIG. 25B shows the signals detected by the firstand second detectors for the second sweep. FIG. 25C and FIG. 25D showthe signals from the first and second detectors after they are convertedinto digital signals for the first and second sweeps, respectively. FIG.25E and FIG. 25F show the signals after the logical OR operation for thefirst and second sweeps, respectively. This embodiment enables alignmentof the light from the first and the second VCL based on the aligning thedigital signals.

A different embodiment of the present invention comprises a referencesignal generator that comprises two etalons, as shown in FIG. 26A. Afiber emits light, which is collimated by a lens into a beam of light.The beam of light is directed to two etalons 2605, 2610 inserted intothe same beam. A first etalon is of a different optical length whencompared to the second etalon. The first etalon has an optical pathlength of 200 microns and the second etalon has an optical path lengthof 197 microns. All surfaces of the etalon are coated with a dielectriccoating to achieve a reflectivity of 0.9 over the spectral range of atleast 1000 nm to 1100 nm wavelength. The etalons are placed in closeproximity to a detector 2615 so as to avoid interfering of the lightfrom the two different paths after passing through the etalons. Thedetector has an active area 2620 that is shared between the light fromthe two etalon outputs. The detector measures the sum of the outputs ofthe two etalons and directs the analog signal to a comparator. FIG. 26B(top) shows the electrical signal that is generated by the detector fromthe incident light over a sweep of one VCL. The detector directs theanalog signal to a comparator. With a threshold value of 0.1, theresulting digital signal is shown in FIG. 26B (bottom). The digitalsignal encodes both of the etalon signals with increasing spacingbetween the etalon peaks. Thus, the direction of the sweep can beascertained from the digital data. The local wavelength can beascertained by the spacing between the etalon peaks.

In one embodiment of the present invention, the two etalons arefabricated from the same piece of glass, similar to as shown in FIG.26A. The surface of the glass is etched to create a shorter optical pathlength in the etched region. Both sides of the glass are coated with areflective surface or surfaces to create the desired reflectivity. Theglass is positioned so that the edge transition between the etchedregion and the unetched region is approximately centered on the detectoractive surface. Projecting a beam that is predominately centered on theedge transition between the etched and non-etched region of the glassdirects the beam also towards the detector active surface. If is alsopossible to use two separate etalons or to generate the different etalondepths by different amounts of etching. It is also possible to projecttwo beams through two different etalons onto the same detector.

The digital data from embodiments of the present invention, for examplethose shown in FIGS. 24-26 can be acquired simultaneously with theinstrument sample data as will be described later and as shown in FIGS.30A-30C. Acquiring the data from the etalon signals with a digital inputcan eliminate the cost of a second analog to digital converter. However,it is also possible to use a second analog input to acquire either thedigital signal from the etalons or an analog signal from the etalons orany other reference signal generator.

An advantage to the embodiments shown, for example in FIGS. 23-26, isthat the reference signal is uniquely associated with the differentportions of wavelength sweep. Consequently, the reference signal used inthe correspondence search can be from either the overlapping region ofthe sweep or the non-overlapping portion of the sweep, making thismethod more flexible than the pure FBG based methods, for example.Further, the signal from the center of the sweep where the sweep poweris largest is more reliable than the signal from the edges of the sweep,improving the reliability and integrity of the signal data. A secondadvantage of the embodiments shown in FIGS. 23-26 is that the referencesignal indicates the directionality of the sweep, and further thelocalized wavelength of any region of the sweep can be determined fromthe reference signal.

FIG. 27 shows an experimental setup and experimental data obtained witha VCSEL sweeping at a 30 kHz rate over a full bandwidth of 120 nm withlinearized scans. FIG. 27A shows an interferometric fringe from a MachZehnder interferometer and an intensity trace of the laser obtained witha photodiode detector. FIG. 27B shows the spectrum of the VCL sourceobtained with an optical spectrum analyzer. FIG. 27C shows anexperimental setup of a reference signal generator comprising a firstand second etalon and first and second detectors, respectively. The twoetalons are of very close optical path length of approximately 3 mm.FIG. 27D shows a schematic diagram of an equivalent optical systemconstructed with Fabry-Perot filters instead of etalons. FIGS. 28A-28Fshow the signals from the two etalons ranging from the start to the endof the sweep. The time difference or separation of the etalon peaksincreases progressively with the sweep such that the relative spacing ofthe peaks can be used to determine the sweep position and the directionof the sweep. In one embodiment of the present invention, the timedifference or sample difference between the first peak from the firstetalon or Fabry-Perot filter and the second peak from the second etalonor Fabry-Perot filter is calculated and the value used as an indicatorof the wavelength at any given portion of the sweep. The estimatedwavelength can be used as the reference signal for any given wavelengthsweep.

FIG. 29 shows the use of a reference signal generator comprising twoetalons or Fabry-Perot filters can be used to wavelength align data fromtwo VCL sources that have a gap in the spectrum. The top two plots showthe raw signal from the first and second etalons and the signal obtainedby thresholding and applying a logic OR to the thresholded data as wouldbe obtained by a single VCL that spanned the entire spectrum. It can beseen that the output of the logic OR operation encodes the position ofthe wavelength sweep. The middle two plots show the raw signal from thefirst and second etalons as would be obtained by a VCL that spanned theshort wavelengths of the spectrum and a VCL that spanned the longwavelength of the spectrum, with a gap in between. The bottom two plotsshow the signal obtained by thresholding the raw data and applying alogic OR to the thresholded data. The unique signature encoded in theoutput signal encodes the wavelength of the sweep and allows the data tobe aligned with respect to wavelength, wavenumber, or phase. Thealignment can be performed even if there is no overlap between thewavelength ranges of the two VCL sources or other wavelength sweptsources. This capability could be useful for example, for obtaining OCTdata of a sample over different and separated wavelength ranges or forobtaining spectroscopy data over different and separate wavelengthswhere it is helpful for the data to be aligned with respect tointerferometric phase, wavelength, or wavenumber.

Embodiments of the present invention have been shown using an A/Dconverter to acquire the signal from reference signal generator. FIGS.30A and 30C shows schematic drawings for embodiments that use a digitalinput to acquire the signal from the reference signal generator. FIG.30A shows an electrical comparator 3005. The output, Vo, is high whenthe voltage at input V+ is larger than the voltage at V−. The output,Vo, is low when the voltage at input V+ is lower than the voltage at V−.A reference signal can be directed to V+ and a threshold voltagedirected at V−. With the reference signal being generated by aFabry-Perot filter or etalon, as shown in FIG. 30B (top), the comparatoroutput is shown for threshold signal values of 0.25V, 0.50V, and 0.75Vin FIG. 30B in the second through fourth rows. The comparator output isconnected to a digital input 3015 on a first-in-first-out (FIFO) queuecircuit. The clock for the A/D converter 3010 and FIFO can be eitherinternally generated or come from an external source, such as an opticalk-clock. The clock of the A/D converter and the FIFO are connected toacquire data at the same time. On each clock cycle, the FIFO circuitclocks in the current value of the digital input and saves the result inthe FIFO queue. The value of the FIFO queue is a binary representationof the reference signal, with each sample point being represented by asingle bit. At the conclusion of the sweep, the value of the FIFO queueis read by a controller (FPGA in FIG. 30C) and used as the referencedigital data for the first sweep and reference digital data for thesecond sweep. Alternately, a FIFO with a smaller number of memoryelements than the sweep can be used and the data periodically pulledfrom the FIFO to the controller, as can be performed to match a highdata rate digital bit stream to the slower clock speeds of the FPGA.Many serializer/deserializer circuits perform this task and can beintegrated into a larger chip, such as an FPGA, or be a dedicated chipof its own. Often the data is pulled from the FIFO queue with a paralleldata bus to allow the input to a FIFO or serializer/deserializer toclock data at a higher rate or different rate than an FPGA's or othercontroller' clock. In the same way as described before for the referencedigital data acquired by an A/D converter, a correspondence match searchcan be performed on the 1-bit binary digital data representation for thefirst sweep and 1-bit binary digital data representation for the secondsweep. The value of the threshold signal can be adjusted to affect thereference signal voltage at which state transitions occur. It ispossible that a reference signal state transition occurs at or near anoptical k-clock state transition, creating an ambiguity as whichwavenumber the reference signal state transition occurred. The thresholdvoltage can be adjusted either up or down until the reference signalstate transition occurs in between optical k-clock transitions. Even ifthere is ambiguity in a state because of noise or close proximity to ak-clock transition, the reference signal generators with multipletransitions can still be properly aligned through the correspondencesearch and exhibits improved robustness to noise compare the referencesignal generators that create only one transition. One embodiment of thepresent invention comprises a comparator and binary queue or FIFO tosample the reference signal for the first sweep and the reference signalfor the second sweep. One embodiment of the present invention furthercomprising a circuit comprising a digital input, wherein the circuit isconfigured to acquire via the digital input and convert the referencesignal for the first wavelength sweep into reference digital data forthe first wavelength sweep and the reference signal for the secondwavelength sweep into reference digital data for the second wavelengthsweep. As an alternative to the Fabry-Perot filter, the reference signalcan be generated from any of the reference signal generators previouslydiscussed in this patent application as they can be similarly voltagethresholded.

The output powers and spectral shape of the first and the second lasersmay not match in the wavelength region where the two sweeps overlap. Itis therefore important that the phase alignment approach be robust tomismatch in the power between the two or more sweeps. Applying the phasematching approach to an embodiment of the present invention using aphase reference generator comprising a Fabry-Perot filter in which thereis a difference in the output power of the first and second sweeps isgenerally robust to power mismatch. Even with a mismatch in themagnitude of the Fabry-Perot transmission peak signal between the firstand second laser sweeps, the minimum sum of squared error signal isstill generally obtained when the two sweeps are properly aligned. Oncealigned, numerical spectral shaping techniques can be used to restorethe fringe envelope to a more desirable Gaussian, Hann, Hamming profile,or other to improve the PSF, as will be described in a later section.Numerical spectral shaping is well known in OCT and spectroscopy.

Applying the phase matching approach to an embodiment of the presentinvention using a phase reference generator comprising a Mach-Zehnderinterferometer in which there is a difference in the output power of thefirst and second sweeps is generally robust. The minimum metric value isassociated with the offset value that properly matches the phase betweenthe two sweeps and the data is generally properly aligned, even forrelatively large mismatch in power.

An embodiment of the present invention using a phase reference generatorcomprising a wavelength meter is robust to differences in power betweenthe first and second lasers. The power normalization inherent in thewavelength meter causes the wavelength meter to generate the same outputvalue for input light of the same wavelength, but different power. Theminimum metric value is associated with the offset value that properlymatches the phase between the two sweeps.

Applying the phase matching approach to an embodiment of the presentinvention using a phase reference generator comprising a fiber Bragggrating in transmission mode in which there is a difference in theoutput power of the first and second sweeps is generally robust, butdepends on the magnitude difference between the two sweeps. For smalldifferences in output power between the first and second sweeps, theinvention using a reference generator comprising a fiber Bragg gratingworks to properly align the data. However, for large mismatch betweenthe output power of the first and second laser, the approach using afiber Bragg grating in transmission mode fails to find the correctoffset value to properly phase align the two sweeps. A near constant DCsignal value resulting from the wide transmission window of the FBGcreates a scenario where the minimum sum of squared differences (SSD)value between the two signals is obtained at an incorrect offset value.It is therefore sometimes preferential to use a FBG in reflection modeto eliminate the DC offset values.

Digitizer subsystems can use an A/D converter that is DC coupled or ACcoupled. Example digitizer subsystems with DC coupled A/D converterinputs include the X5-400M sold by Innovative Integration or ATS 9350sold by Alazar Technologies, Inc. DC coupled A/D converters preserve theDC information of the signal, but require DC to high bandwidthelectrical gain or buffering stages, which often introduce harmoniccontent into the signal during the amplification or buffering process.Therefore, AC coupled A/D converters are preferred for high bandwidthapplications, producing less harmonic distortion and using less power.Example digitizer subsystems that offer AC coupled A/D converter inputsinclude the X6-GSPS sold by Innovative Integration and ATS9350 fromAlazar Technologies.

AC coupling of the signal to the A/D converter can also improve therobustness of the phase matching approach. In particular, consider afailed attempt in the approach of using a phase reference generatorcomprising a FBG in transmission mode with a large difference in powerbetween the first and second sweep when used with a DC coupled A/Dconverter. An alternate embodiment that comprises a high pass filterapplied to the output of the detector measuring the light from the FBGeliminates the large DC component of the FBG signal to emphasize thetransient. An embodiment of the present invention comprising a high passfiltered signal from an FBG is robust to differences in power betweenthe first and second lasers.

Similar results are achieved when using the high pass filtered signalsfrom the Fabry-Perot filter and the Mach-Zehnder interferometer.However, the signal from the wavelength meter is predominately lowfrequency containing no characteristic transient occurring to indicatewavelength, phase, or wavenumber, so is not suitable for AC coupling.

The high pass filtering of the reference signals can be performed withanalog components, with digital components, or in digital processing.One embodiment of the present invention comprises a high pass filterconstructed of analog components. Another embodiment of the presentinvention comprises a high pass filter implemented with digitalfiltering components. One more specific embodiment of the presentinvention comprises a digital filter implemented in an FPGA, ASIC, DSP,processor, microcontroller, or any other digital processing unit. Oneembodiment of the present invention comprises an A/D converter with A/Ccoupled input to high pass filter the reference signals. Anotherembodiment of the present invention comprises an A/D converter with DCcoupled input and analog high pass filter to filter the referencesignals. Another embodiment of the present invention comprises a DCcoupled A/D converter and a processor or other digital electroniccircuit to digitally filter the reference signals. Common digital filterimplementations known in the art of filter design are finite impulseresponse (FIR) and infinite impulse response (IIR) filters, both oreither if which can be used with the present invention. One embodimentof the present invention comprises a reference high pass filter 2145configured to filter the reference signal for the first wavelength sweepand the reference signal for the second wavelength sweep, or to filterthe reference digital data for the first wavelength sweep and thereference digital data for the second wavelength sweep. One embodimentof the present invention is a method comprising filtering with a highpass filter at least one of: the reference signal for the firstwavelength sweep, the reference signal for the second wavelength sweep,the reference digital data for the first sweep, and the referencedigital data for the second sweep.

The effects of ASE from an optional optical amplifier that reaches thereference signal generator should be considered. The reference signalgenerators comprising a Fabry-Perot filter, an FBG and interferometerare least affected by ASE. The non-interferometric wavelength meter ofFIG. 19G is potentially affected by ASE as any optical amplifier lightthat is outside the VCL tuning band affects the output signal topotentially produce a wrong measurement. This suggest that theconfigurations shown in FIGS. 11A, 11C, and 11D are preferable to theconfiguration shown in FIG. 11B because the light used to generate thereference signal is obtained directly from the VCL, which is essentiallypurely tuned light. ASE can create a DC offset for the Fabry-Perotfilter, an FBG and interferometer configurations, suggesting that highpass filtering of the reference signal or reference digital data isgenerally preferred.

The examples so far have predominately described the scenario where theA/D converter is clocked with an optical k-clock signal such that thesamples occur at equal or repeatable k intervals (Note, however, thatthe intervals can vary from equal spacing in the presence of dispersionin the k-clock interferometer). It is also possible to clock using afixed internal clock source. In either case, one embodiment of thepresent invention comprising a primary analog to digital converter 505within the digitizer subsystem, wherein the primary analog to digitalconverter is configured to convert the sample signal for the firstwavelength sweep into sample digital data for the first wavelength sweepand the sample signal for the second wavelength sweep into sampledigital data for the second wavelength sweep. In one embodiment of thepresent invention, the primary analog to digital converter and thedigital input are simultaneously clocked. A second analog to digitalconverter can be used to digitize the reference signal. One embodimentof the present invention comprises a secondary analog to digitalconverter 510 in the digitizer subsystem, wherein the secondary analogto digital converter is configured to convert the reference signal forthe first wavelength sweep into reference digital data for the firstwavelength sweep and the reference signal for the second wavelengthsweep into reference digital data for the second wavelength sweep. Inone embodiment of the present invention, the primary analog to digitalconverter and secondary analog to digital converter are simultaneouslyclocked. The term simultaneously clocked is common language in the fieldof data acquisition to indicate that the two or more analog to digitalconverters are clocked with a shared clock source. The clock source maybe distributed or replicated and there may be additional small delays onthe order of a fraction of the clock cycle because of electricalpropagation times in the electrical connections and electronics.Simultaneous clocking is helpful for aligning the data for both the caseof the optical k-clock and the fixed internal clock scenarios. Oneembodiment of the present invention comprises an optical k-clockgenerator 2135 configured to clock the primary analog to digitalconverter. Another embodiment of the present invention comprises aninternal clock generator 3105 configured to clock the primary analog todigital converter.

Two Channel Acquisition with Internal Clock

An optical k-clock requires high speed electronics, careful path lengthmatching, and precise timing to generate transform limited or neartransform limited OCT point spread functions. Further, some A/Dconverters do not properly function when the clock signal deviates from50% duty cycle or the clock frequency changes, as is common in opticalk-clock applications where the sweep trajectory is often non-linear inwavenumber (k). In applications when k-clocking is not desirable, suchas when using high A/D conversion rates or when a less complicatedimplementation is desired, an internal A/D clock can be preferred. Oneembodiment of the present invention is a method comprising the step ofconverting the sample signal for the first wavelength sweep into sampledigital data for the first sweep performed with predetermined timeinterval spacing between sample points. One embodiment of the presentinvention uses two channels of simultaneously sampled A/D converterswith the clock source generated internally at either a fixed frequencyor predetermined frequency profile. One embodiment of the presentinvention comprises an internal clock generator, wherein the internalclock generator clocks the primary analog to digital converter. FIG. 31shows an example system with internal clock 3105. Output power from aVCL source is split by fiber couplers into an imaging interferometer, acalibration interferometer acting as a phase calibration generator, anda reference signal generator. An electrical trigger connects the VCLsource to the digitizer subsystem. A schematic diagram of a digitizersubsystem 3205 and an experimental implementation are shown in FIGS.32A-32B. A two channel 3210, 3215, 14 bit analog to digital converterchip (Analog Devices 9680) is mounted on a daughterboard on aproprietary carrier board (Thorlabs ThorDAQ) which comprises an FPGA(Xilinx Kintex 7) and PCIe computer interface data bus. The digitalinput is simultaneously sampled with the analog data by making use ofthe input serializer/deserializer (ISERDES) 3225 on the Kintex 7, whichacts as the digital input FIFO or binary queue of the present invention.The digital input FIFO is clocked off the same clock 3220 as the analogto digital converter. An internal clock source is used to sample theanalog data from the two channels and the digital data allsimultaneously at 500 MSPS. A record of 2048 samples is acquired onevery rising edge transition of the trigger signal. A software commandis issued from a host pc computer to start the acquisition, after which,a total of 1024 sequential records are acquired for each channel. Thecollection of records, might, for example, represent the data containedin an OCT B-scan. The electrical trigger signal is used to initiateacquisition of each record. In data acquisition systems, it is common tostore and send data in 16 bit units for reasons of memory alignment.With only 14 bits of analog data for each channel, the remaining bitscan be used to store the digital data. FIG. 33 shows how the digitaldata is packaged with the analog data to preserve the temporalsynchronicity between the analog and digitally sampled data. Two datastreams result, one for the first analog input and one for the secondanalog input. At each sample point, the value of the analog input isencoded in the lower most 14 bits and the value of the digital input isencoded in the highest most bit. Other A/D bit depths and samplingspeeds are possible. FIG. 34 shows the interconnections and signalsbetween the VCL source, the experimental optical setup, and thedigitizer subsystem. The VCL source comprises a VCSEL operating at a 100kHz sweep repetition rate. An electrical trigger signal indicates thestart of the sweep. The reference signal generator comprises a 30:70fiber coupler, three FBGs at wavelengths of 1028 nm, 1047 nm, and 1079nm and a 15 MHz bandwidth amplified InGaAs diode detector. The FBGs arechained together and operated in reflection mode using the 30:70 fibercoupler such that a rapid rising edge electrical signal transitionoccurs as the VCSEL light sweeps and reaches and reflects from the FBGwavelength into the diode detector. In this experiment, the logicallevel high threshold of the 3.3V CMOS logic level input of the digitalinput on the FPGA board acted as the comparator, registering a highvalue when the analog voltage from the InGaAs detector was above the3.3V CMOS logic level high threshold level.

A typical use scenario is to acquire a number, n_(sweeps), of sequentialsweeps and to phase stabilize or wavelength align all of the sweeps toeach other. FIG. 35A shows the raw data from two sweeps, {right arrowover (S)}₁ and {right arrow over (S)}₂ over the same wavelength rangeacquired sequentially that are plotted on top of each other with theresult of the digital input in the top plot and the analog input in thebottom plot. The first sweep acquired at a first time point is shown asa solid line and the second sweep acquired at a second time point isshown as a dashed line. The zoom on the analog data near the 1028 nm FBGshown in FIG. 35B (bottom) shows the interferometric fringe from thereference MZI. Because of sweep to sweep variation and triggeruncertainty, the fringe from the first sweep is almost 180 degrees outof phase with the fringe from the second sweep and it is not clear bylooking at the analog data alone if the second fringe should be advancedor delayed relative to the first fringe to phase align the data. Asimilar case of ambiguity exists in FIG. 35C (bottom) for the 1047 nmFBG and FIG. 34D (bottom) for the 1079 nm FBG, which may be nearlyaligned or nearly a cycle or integer multiple of a cycle off in phasealignment. The ambiguity can be removed by looking at the digital datashown in FIGS. 35B-35D (top). It is clear that the second fringe (dashedline) needs to be advanced (shifted left) to properly align the datawithout ambiguity. A practical instrument may not require three FBGs asone FBG in many cases will be adequate. Multiple FBGs or signals derivedfrom an etalon, Fabry-Perot filter, or reference interferometer thatgenerate multiple signature features in response to a wavelength sweepoffer the potential of redundancy in alignment data, which can help toreduce errors due to noise in the signals if the multiple features arematched. Also in a practical system, it is desirable to match fiber andelectrical cable lengths so that the propagation time for the all of theanalog and digital channels are the same. In this experiment,differences in fiber lengths and cable lengths resulted in the channel 1(reference MZI or calibration interferometer) leading channel 2 (sampleinterferometer) by about 4 ns. Difference in propagation time betweenchannels is common in real system and can be compensated numerically.Performing a fast Fourier transform (FFT) of the channel 2 data,multiplying the complex result by a ramp in phase equivalent to 4 ns,then performing an inverse FFT and retaining the real component allowsfor ideal and subpixel time shifts, as is known in the art of signalprocessing. With the data in channel 1 and channel 2 now aligned intime, the rising edge transition of the digital data associated with the1049 nm FBG is located for the first and the second sweeps. A subset ofdata from each channel 1 sweep, {right arrow over (A)}_(i), where i=1,2, 3, . . . , n_(sweeps), is selected by counting backwards from therising edge transition of the digital data to define a starting indexand forwards from the rising edge transition of the digital data todefine an ending index. Retaining 850 samples before and 1028 samplesafter the rising edge transition captures the majority of the usefulfringe while avoiding the case of indexing outside of the valid datarange due to sweep-to-sweep variation. The results of the data subsetselection are shown in FIG. 36A. With this corrective step, the phase ofthe MZI calibration fringe is well aligned between the first and secondsweeps and there is less than 1 sample point of phase misalignment atthe location of the 1049 nm FGB (FIG. 36B). The phase would be expectedto be aligned at the location of the FBG because as long as the MZI doesnot change path length, the phase should be the same at the samewavelength for repeated scans, even if the scan trajectory changes. Theslight mismatch in phase is mostly due to the asynchronous clocking andis expected. Phase in this experiment is roughly aligned away from theFBG signal (FIG. 36C), but it is not necessarily expected to be alignedif there is sweep-to-sweep variation as the phase evolution curve willbe different for each sweep. A Hilbert transform followed by phaseunwrapping can be performed to the fringe on analog channel 1 obtainedat the first time point to obtain the fringe phase as a function of datapoint, {right arrow over (H)}₁, as is known in the art of signalprocessing. The resulting phase at the sample index locationcorresponding to the rising edge of the FBG signal can be determined andsaved in a variable to represent the nominal phase at the FBG locationof the first sweep, which is 773.76 radians for this experimentalexample, as indicated by the horizontal dashed line in FIG. 36D and thezoomed in inset, labeled, p₀. A starting phase, p_(start), and endingphase, p_(end) can also be determined and selected to span as much ofthe fringe as possible, but to stay within the phase limits consideringsweep to sweep variation such that any experimental sweep is expected tospan at least a range greater than p_(end)−p_(start). The values of p₀,p_(start), and p_(end) form the absolute range over which fringerecalibration will take place and apply to all sweeps in an acquisition,for example a multi-sweep OCT or spectroscopy data set that needs to bephase or wavelength stabilized. In the case of sweep-to-sweep variation,it is not clear at which phase the fringe will start for any given sweepand the Hilbert transform with phase unwrapping may generate a phaseevolution curve, H_(i), that is an integer multiple of 2π larger orsmaller than the nominal phase. In order to align the phase for anygiven sweep, the phase evolution curve can be adjusted by adding orsubtracting integer multiples of 2π from every sample point in order tominimize the difference in the value of the phase at the rising edge ofthe digital data compared to the value of p₀. For any given sweep, leti_(rise) be the index of the rising edge transition in the digital dataand {right arrow over (p)} be the vector of the phase evolution curvefor that given sweep. The goal is to choose m such that the value of({right arrow over (p)}[i_(rise)]+m2π)−p₀ is minimized, then to add thevalue of mπ to each element of the vector, {right arrow over (p)} togenerate a corrected phase evolution curve {right arrow over (p)}_(i)^(corrected). In the example shown in FIG. 35D in the zoomed inset, itcan be seen that for the phase of the second sweep, H₂, the value of m=0best aligns the phase data as the error in phase at the index of therising edge of the digital data is very small. Once the 2π ambiguity hasbeen removed, the sequence of fringes acquired at different time pointscan be processed by interpolating the fringe to be equal k intervalsover the correct phase span with a cubic, linear, or other interpolationscheme known in signal processing. An interpolation generally takes asinput a vector of known x values, {right arrow over (x)}_(in), withcorresponding y values, {right arrow over (y)}_(in), and a vector ofknown x values at which to calculate the interpolation, {right arrowover (x)}_(out), to generate a vector of interpolated y values, {rightarrow over (y)}_(out), such that:{right arrow over (y)} _(out)=ƒ({right arrow over (x)} _(in) ,{rightarrow over (y)} _(in) ,{right arrow over (x)} _(out)).  Eq. 7

It is desired that all sweeps span the same phase range with the sameabsolute phase, so {right arrow over (x)}_(out) is a vector with thedesired number of interpolation points with nominally equal spacing fromp_(start) to p_(end), which will be constant and apply to all of thesweeps in a data set. For every individual sweep in the data set, {rightarrow over (x)}_(in) is the phase evolution curve, {right arrow over(p)}_(i) ^(corrected) and {right arrow over (y)}_(in) is the subset ofchannel 2 data corresponding to the sampled data, {right arrow over(A)}_(i). The alignment parameters are, in this example of aligning twofringes spanning the same wavelength range that are acquired atdifferent time points, the inputs to the interpolation function.

For the values of p_(start)=10 rad and p_(end)=1500 rad, examples of theinterpolated fringe are shown in FIG. 37A. Zoomed in panels 37B and 37Cshow that the fringe is now phase aligned (phase stabilized) between thesweep acquired at the first time point (solid line) and the second timepoint (dashed line), as observed by the close phase alignment and almostperfect overlapping of the fringe data. Fourier transforming yieldsnearly identical phase stabilized OCT point spread functions, as shownin FIG. 37D. One embodiment of the present invention comprising a singleVCSEL source, an imaging interferometer, a calibration interferometer,and a digital input that is synchronously clocked with the analog todigital converter. The clock can be derived from an optical k-clock orfrom an internal clock source. One embodiment of the present inventionis an optical instrument comprising a VCL source configured forgenerating tuned emission over a wavelength range to generate a firstwavelength sweep at a first time point and a second wavelength sweep ata second time point and an optical system configured for delivering atleast a portion of the first wavelength sweep and at least a portion ofthe second wavelength sweep to a sample and a reference signal generatorconfigured for receiving at least a portion of the tuned emission fromthe first wavelength sweep to generate a reference signal for the firstwavelength sweep and at least a portion of the tuned emission from thesecond wavelength sweep to generate a reference signal for the secondwavelength sweep and a sample detector configured for detecting tunedemission from the first wavelength sweep that is affected by the sampleto generate a sample signal for the first wavelength sweep and tunedemission from the second wavelength sweep that is affected by the sampleto generate a sample signal for the second wavelength sweep and adigitizer subsystem configured for converting the sample signal from thefirst wavelength sweep into sample digital data for the first wavelengthsweep, the sample signal for the second wavelength sweep into sampledigital data for the second wavelength sweep, the reference signal forthe first wavelength sweep into reference digital data for the firstwavelength sweep, and the reference signal for the second wavelengthsweep into reference digital data for the second wavelength sweep and analignment processor configured for using the reference digital data forthe first wavelength sweep and the reference digital data for the secondwavelength sweep as input to process the sample digital data for thefirst wavelength sweep and to process the sample digital data for thesecond swept wavelength sweep to generate output digital data, whereinthe resulting output digital data is aligned with respect to at leastone of: wavelength, wavenumber, and interferometric phase to wavelength,wavenumber or phase stabilize the first wavelength sweep to the secondwavelength sweep.

FIGS. 38A-38C show an example of combining two different sweeps spanningdifferent wavelength ranges with a small amount of overlap between thesweeps. A VCSEL operating at 1050 nm wavelengths is swept with the lightdirected to a 70:30 coupler in which 70% of the light proceeds to asecond 50:50 coupler which divides the light to two interferometers. Afirst interferometer is connected to analog channel 1 and the secondinterferometer is connected to analog channel 2 of a digitizer subsystemoperating with an internal clock that samples at 500 MSPS. The 30%portion of light is directed to an FBG at 1049 nm used in reflectionmode so that the reflected light travels back through the 70:30 couplerto a 15 MHz amplified InGaAs diode detector. The experiment and VCSELoperating conditions are the same as for the data shown in FIGS.37A-37D. The output of the detector is connected to a digital input onthe digitizer subsystem that is simultaneously sampled with the twoanalog channels. As shown in FIG. 38A, the digitizer subsystem is set toacquire a first sweep, sweep 1 and a second sweep, sweep 2, in which thefirst 860 data points of the first sweep are retained for sweep 1 andthe last 1038 samples are retained for sweep 2. Sweep 1 is acquiredduring a different sweep than sweep 2 so that the phase is notcontinuous between the two sweeps. The rising edge transitions of thedigital signals are used to align sweep 1 to sweep 2, as shown in FIG.38B. Because sweep 1 was acquired from a different physical VCSEL sweepthan sweep 2, sweep-to-sweep variation and asynchronous clocks betweenthe VCSEL source and the digitizer subsystem cause the phase of sweep 2to differ from the phase of sweep 1 in the overlapped spectrum, as seenin the zoomed in plot of FIG. 38B. Let i₁ ^(FBG) be the index of therising edge transition in the digital data for sweep 1 and i₂ ^(FBG) bethe rising edge transition in the digital data for sweep 2. A Hilberttransform is performed on the calibration interferometer channel,channel 1 in FIG. 34, for sweep 1 and sweep 2 in order to generate phaseevolution curves {right arrow over (p)}₁ and {right arrow over (p)}₂,respectively. There may be multiples of 2π difference between the phaseof the first and the phase of the second sweep at the location wherethey are to be aligned, which are corrected as follows. The differencein the phase between the first and second sweep at the shared locationof the digital data rising edge transition is calculated asΔp_(junction){right arrow over (p)}₂└i₂ ^(FBG)┘−{right arrow over(p)}₁└i₁ ^(FBG)┘. A rounded closest estimate of the phase is calculatedas Δp_(round)=round(Δp_(junction)/(2π)). A phase correction iscalculated as Δp_(correction)=2πΔp_(round) and a new adjusted phase forthe second sweep calculated by subtracting the phase correction fromevery vector element of the phase curve as {right arrow over(p)}_(c)={right arrow over (p)}₂−Δp_(correction). An anchor phase iscalculated as p₀={right arrow over (p)}₁└i₁ ^(FBG)┘ and a start phase,p_(start), and end phase estimate, p_(endest) defined such that thestart phase is close to the start of valid phase data in the first sweepand the end phase estimate is close to the end of valid data for thecombined phase of the first and second sweeps. Similar to as was shownin FIG. 36D, the start phase and end phase estimate must be selected toensure that under sweep-to-sweep variation, valid phase ranges will beobtained to prevent indexing or interpolating outside of valid data.Sweep-to-sweep variation can be quantified experimentally, and throughstatistics and application of factors of safety, safe phase ranges canbe determined. A number of desired interpolation points for sweep 1 isdefined, n_(sweep1). The interpolated phase per sample point iscalculated as d_(ps)=(p₀−p_(start))/n_(sweep1). To preserve the samplespacing with respect to phase, the number of interpolated points forsweep 2 is calculated as n_(sweep2)=round((p_(endest)−p₀)/d_(ps)) andthe ending phase for sweep 2 as p_(end)=p₀+n_(sweep2)d_(ps). At thispoint, the interpolation can be performed to generate sample data thatis linear in wavenumber (k) and phase or wavelength aligned at theboundary of the two sweeps. Interpolation vectors can be defined as{right arrow over (x)}_(out) ¹ being a vector having nominally equallyspaced sample points over the interval from p_(start) to p₀ withn_(sweep1) sample points and {right arrow over (x)}_(out) ² being avector having nominally equally spaced sample points over the intervalfrom p₀ to p_(end) having n_(sweep2) sample points. Remembering that thephase reference data from channel 1 is used to align the sample relateddata of channel 2, the input data to the interpolation defined as:{right arrow over (x)}_(in) ¹ is the vector of phase data from sweep 1acquired on channel 1, {right arrow over (y)}_(in) ¹ is the vector ofsample data acquired on channel 2, {right arrow over (x)}_(in) ² thevector of phase data from sweep 2 acquired on channel 1, and {rightarrow over (y)}_(in) ² is the vector of sample data from sweep 2acquired on channel 2. Phase aligned sample data for the first sweep,{right arrow over (y)}_(out) ¹, is generated by the interpolation stepdefined by Eq. 7 as {right arrow over (y)}_(out) ¹=ƒ(x_(in) ¹, y_(in) ¹,x_(out) ¹) and phase aligned sample data for the second sweep, {rightarrow over (y)}_(out) ², is similarly generated as {right arrow over(y)}_(out) ²=ƒ({right arrow over (x)}_(in) ², {right arrow over(y)}_(in) ², {right arrow over (x)}_(out) ²). At this point, {rightarrow over (y)}_(out) ¹ and {right arrow over (y)}_(out) ² have a sharedsample point, so the complete concatenated sample data, {right arrowover (y)}_(concat)=└{right arrow over (y)}_(out) ¹, {right arrow over(y)}_(out) ^(2*)┘, can be formed by removing the first data point of{right arrow over (y)}_(out) ² to form {right arrow over (y)}_(out) ²*.Alternately, the last data point of {right arrow over (y)}_(out) ² couldbe removed or the overlapping data averaged. The alignment parametersare, in this example of aligning two fringes spanning differentwavelength ranges, the inputs to the interpolation function. Anequivalent formulation exists for the non-uniform discrete Fouriertransform or non-uniform fast Fourier transform, as known in the art ofsignal processing, and are also included in the present invention.

For the experiment with p_(start)=10 rad, p_(endest)=1500 rad, andn_(sweep1)=900, the direct amplitude result of a fast Fourier transformof the concatenated fringe zero padded 20 times to show the finestructure is shown in FIG. 38C (left), which can be seen to be asymmetric and well shaped OCT point spread function (PSF), indicatingthe quality of the phase continuity performed. The large sidelobes arean expected result of the fringe envelope, as shown in FIG. 38A, channel2. Spectral shaping, as is well known in the art of OCT, can reducesidelobes with a tradeoff to axial resolution. A Hanning window spectralshaping was applied to the concatenated fringe to generate the PSF shownin FIG. 38C (right). Once the essential characteristic of phase orwavelength continuity has been established, other improvements wellknown in the art of OCT, such as dispersion compensation of the sampledata, dispersion compensation of the reference data, signal propagationtime compensation, detector and electronics phase or amplitudecompensation, and others can be applied as appropriate.

Acquisition System Enhancements

Referring to FIG. 39A, it has been shown that embodiments of the presentinvention can be used to align multiple sweeps with similar or the samewavelength ranges from the same VCL source or other wavelength sweptsource with respect to interferometric phase, wavelength, or wavenumber.Sample digital data associated with a first wavelength sweep acquired ata first time point and sample digital data associated with a secondwavelength sweep acquired at a second time point can be aligned based onreference digital data for the first sweep and reference digital datafor the second sweep. The wavelength range of the first wavelength sweepand the second wavelength sweep will most commonly be the same orsimilar. Motivation for using similar wavelength ranges could be togenerate phase stabilized OCT data or to allow averaging of spectroscopydata. Motivation for using different wavelength ranges could be tocompare a high resolution spectroscopy measurement acquired over alonger time period to a lower resolution acquired over a shorter timeperiod. Referring to FIG. 39B, it has been shown that embodiments of thepresent invention can be used to align sweeps from different VCL sourcesor other wavelength swept sources with respect to interferometric phase,wavelength, or wavenumber. Sample digital data associated with a firstwavelength sweep from a first VCL source or wavelength swept source canbe aligned with sample digital data associated with a second VCL sourceor wavelength swept source based on reference digital data for the firstsweep and reference digital data for the second sweep. The wavelengthrange and other sweep characteristics of the first VCL source orwavelength swept source and the second VCL source or wavelength sweptsource can be the same, but will often be different. Motivation forusing two different VCL sources or wavelength swept sources with similarsweep characteristics might be to increase sweep repetition rates byinterleaving sweeps or to extend lifetime of an instrument, for example.Motivation for using different wavelength ranges would be to achievefiner OCT axial resolution or to span a larger spectrum forspectroscopy. Although FIGS. 39A-39B are shown with a Fabry-Perot oretalon based reference signal generator, other reference signalgenerators achieve the same fundamental goals. Various enhancements tothe basic apparatus and method are now described.

The sweep-to-sweep variation of a MEMS-tunable VCSEL is generally alarger contributor to the uncertainty in starting wavelength,wavenumber, or interferogram phase of each sweep compared to the sampleuncertainty associated with the electrical trigger signal jitter. Theelectrical trigger signal is generated in synchronization with the MEMSactuator drive waveform such that the dynamic response of theMEMS-tunable VCSEL, and in particular the oscillations at the multipleresonant frequencies, result in the sweep trajectory changingsweep-to-sweep. One embodiment of the present invention comprises anoptical wavelength trigger, as shown in FIG. 40. The optical wavelengthtrigger generates an electrical trigger signal in response to theMEMS-tunable VCSEL emitting at a particular wavelength. The effect ofthe optical sweep trigger is to predominately remove much of theuncertainty in emission wavelength to reduce jitter in the acquiredsignals. The reduction in uncertainty is beneficial as the size of thecorrespondence search window can be reduced for improved computationalefficiency. In one embodiment of the present invention, the opticalsweep trigger is a Bragg grating or fiber Bragg grating or equivalentand trigger detector. In another embodiment of the present invention,the optical sweep trigger is a Fabry-Perot filter, Fabry-Perot etalon,or Fabry-Perot interferometer. In another embodiment of the presentinvention, the optical sweep trigger comprises a grating and detector.In another embodiment of the present invention, the optical sweeptrigger comprises a notch or bandpass optical filter. Any optical devicethat generates a signal at a particular or repeatable wavelength can beused in the present invention as an optical sweep trigger.

FIG. 41A shows a schematic diagram of a digitizer subsystem. The A/Dconverter chip in this embodiment of the present invention includes 2input channels. The clock source can either be internal or external. AnFPGA is connected to the A/D converter via a data bus and signalconnections. The FPGA controls the A/D converter and receives digitaldata from the A/D conversions. The FPGA can operate on the digital dataand can transmit the data over a data bus to the host instrument system.In many implementations of digitizer subsystems, the A/D converter isalways active to be sampling and generating digital data in response tothe clock signal. The FPGA monitors the trigger input signal and eithertransmits the digital data over the data bus to the host instrument ordiscards the data. In most implementations, the FPGA discards digitaldata until the FPGA detects a trigger signal. On detecting the triggersignal, the FPGA starts to either save the data to memory or to senddigital data over the data bus to the host instrument. The FPGA saves orsends a predetermined number of sample points for each trigger event andthen waits for the next trigger signal. The collection of predeterminednumber of data points acquired for each trigger event is called arecord. It is also possible to implement a memory buffer in the FPGA ina first-in-first-out (FIFO), scrolling, or circular memory bufferconfiguration. The memory buffer enables the identification andtransmission of pre-trigger samples, which are data points collectedinto the record immediately before the trigger event. Data pointscollected into the record immediately following the trigger event arecalled post trigger samples. FIG. 41B shows a data record comprisingonly post-trigger samples (top) and a data record comprising pre-triggerand post-trigger samples (bottom). The ability to acquire pre-triggerand post-trigger samples enables an efficient implementation of anembodiment of the present invention. A fiber Bragg grating withreflective wavelength falling in between the wavelengths of overlapbetween the first and second laser sweeps is connected to a triggerdetector. The trigger detector is connected to the trigger input of thedigitizer subsystem. By configuring the digitizer subsystem to acquire apredetermined number of pre-trigger and post-trigger samples in responseto the trigger signal, the first and second sweeps of the laser can beacquired with minimal trigger jitter, as shown in FIG. 41C. FIG. 41C(top) shows the OCT fringe data for the first and second sweeps. FIG.41C (middle) shows the fiber Bragg grating signal for the first andsecond sweeps. FIG. 41C (bottom) shows the high pass filtered signalfrom FIG. 41C (middle). Using the optical trigger reduces theuncertainty in the fringe alignment, which can reduce the size of thesearch window required to identify a region of match between thereference signals and improve processing time. An electrical trigger canalso be used with pre and post trigger acquisition.

In the case of the reference signal generator being an MZI, it ispossible to configure the MZI to generate a fringe period that issignificantly larger than the expected sweep-to-sweep jitter. FIG. 42A(top) shows a simulation of a first sweep from a first VCL source and asecond sweep from a second VCL source that have different centerwavelengths, but overlap in the spectrum. A trigger signal as would begenerated by an FBG in reflection mode or an electrical trigger is shownin FIG. 42A (bottom). The optical path length of the MZI has been set sothat the period of the interferometric fringe is larger than theexpected jitter in the trigger signal. This has the effect ofeliminating the possibility of a 2π ambiguity in the reference dataphase, thereby simplifying the apparatus, approach and method. In FIG.42B, J1 represents the jitter of the VCL of the first sweep, P1represents the period of the interferometric fringe at or near thetrigger signal of the first sweep, J2 represents the jitter of the VCLof the second sweep, and P2 represents the period of the interferometricfringe at or near the trigger signal of the second sweep. Measurementsof the VCL can be experimentally performed to characterize theuncertainty in trigger position relative to the interferometric fringe,the standard deviation calculated, and confidence intervals defined withappropriate factors of safety to determine an expected worst case jittermagnitude over all sweeps to define the jitter of the VCL. If the phaseof the interferometric fringe is set to be larger than the jitter of theVCL, then the 2π ambiguity in phase can be eliminated. Similaradvantages can be obtained with the reference generator being aFabry-Perot filter or etalon. Embodiments comprising a phase calibrationgenerator similarly benefit. In these cases, the search window can bereduced or the step of determining a multiple of 2π correction to thephase removed from the processing steps performed by the alignmentprocessor. One embodiment of the present invention comprises a referenceinterferometer, wherein the reference interferometer generates a fringeperiod that is greater than the sweep-to-sweep jitter of the VCL sourceor other wavelength swept source. Another embodiment of the presentinvention comprises a reference Fabry-Perot filter or reference etalon,wherein the transmission peak spacing of the reference Fabry-Perotfilter or reference etalon is larger than the sweep-to-sweep jitter ofthe VCL source or other wavelength swept source. Another embodiment ofthe present invention comprises an interferometer as the phasecalibration generator, wherein the phase calibration generator generatesa fringe period that is greater than the sweep-to-sweep jitter of theVLC source or other wavelength swept source.

Data throughput from the digitizer subsystem to the host instrument canbe constrained by the data bus connection and the size of acquisitionconstrained by memory limits. FIG. 43 shows how optimal selection of therecord size can reduce the data transmission, data storage, andprocessing requirements. Whereas the entirety of the relevant section ofthe OCT fringe for the first and second sweeps must be collected usingn₁₁ and n₁₂ samples, respectively, as shown in FIG. 43, only a fewsamples of data need be collected from the reference signal in order toperform the wavelength, wavenumber, or interferogram phasecorrespondence match. In one embodiment of the present invention, thenumber of samples, n₂₁, acquired, processed, or transmitted in thereference signal from the first sweep is less than the number ofsamples, n₁₁, acquired, processed, or transmitted in the signal datafrom the first sweep. In another embodiment of the present invention,the number of samples, n₂₂, acquired, processed, or transmitted from thereference signal of the second sweep is less than the number of samples,n₁₂, acquired, processed, or transmitted from the instrument signal. Oneembodiment of the present invention operates with: (a) the number ofdata points 4305 in the sample digital data for the first wavelengthsweep is larger than the number of data points 4315 collected,processed, or transmitted in the reference digital data for the firstwavelength sweep or (b) the number of data points 4310 in the sampledigital data for the second wavelength sweep is larger than the numberof data points 4320 collected, processed, or transmitted in thereference digital data for the second wavelength sweep or (c) the numberof data points 4305 in the sample digital data for the first wavelengthsweep is larger than the number of data points 4315 collected,processed, or transmitted in the reference digital data for the firstwavelength sweep and the number of data points 4310 in the sampledigital data for the second wavelength sweep is larger than the numberof data points 4320 collected, processed, or transmitted in thereference digital data for the second wavelength sweep.

Many OCT applications have limits on the exposure of light that can beprojected onto the sample. For example, ophthalmic OCT applications areoften governed by permissions, approvals, and regulations that limit thelight exposure on the eye. As an example, instrumentation often adhereto guidelines described by the American National Standards Institute(ANSI), “American National Standard for Safe Use of Lasers,” ANSIZ136.1. In one embodiment of the present invention, light to theinstrument is turned off while light to the reference signal generatorremains on in order to minimize light exposure to the sample while stillgenerating a reference signal that can be used for a correspondencematch. FIG. 44A shows a schematic diagram of an embodiment of thepresent invention. Two electrically pumped VCSELs, eVCSEL 1 and eVCSEL2, are connected to a 50:50 fiber coupler. One output of the fibercoupler directs light from the eVCSELs to a monitoring, diagnostic, andauxiliary function subsystem. A portion of the light from themonitoring, diagnostic, and auxiliary function subsystem is directed toa reference signal generator comprising a Fabry-Perot filter anddetector. The other output of the 50:50 fiber coupler directs light fromeVCSEL 1 and eVCSEL 2 to an isolator. Light from the isolator isdirected to a booster optical amplifier. A current driver is connectedto the BOA which controls the gain of the BOA and which can be used toeffectively turn the BOA emission on and off. Each of eVCSEL 1 andeVCSEL 2 can be turned on and off by energizing or de-energizing aconstant current driver attached to eVCSEL 1 and eVCSEL 2. The emissionstate of eVCSEL 1 and eVCSEL 2 determine the presence of light in theFabry-Perot filter and the duration of the reference signal, as shown inFIG. 44B (bottom). The emission state of the BOA determines the presenceof light in the instrument sample path. Turning the BOA off a length oftime before turning either eVCSEL 1 or eVCSEL 2 off enables there to bea reference signal without any exposure to the sample, as shown in FIG.44B. FIG. 45A shows the OCT fringe obtained by a single mirrorreflection (top) and the reference signal (bottom) as sampled usingoptical k-clocking. FIG. 45B shows a zoomed in view of the OCT fringeand the reference signal in which it can be seen that the number ofoverlapping of samples in the OCT interferogram is much less than thenumber of overlapping samples in the reference signal. The small numberof overlapping samples in the OCT interferogram is associated withminimizing the exposure on the sample. The larger number of samplesassociated with the reference fringe aid in performing thecorrespondence match process. A timing diagram showing how a reductionof light to the sample can be achieved by switching off the light to thespecimen while still generating light in the reference path to enablecollection of enough samples for proper data alignment is shown in FIG.46.

It is possible that the power output of the first VCL (either directlyor optically amplified) be different from the power output from thesecond VCL (either directly or optically amplified) causing theresulting aligned data to have a discontinuity in amplitude. A step ofnumerical spectral shaping of the output digital data can be performedto generate the desired power vs. wavelength profile. It is alsopossible to control the current to an optical amplifier, for example theBOA in FIG. 11, in order to compensate for different VCL output power oroptical amplifier output power to generate the desired power vs.wavelength profile with a smooth transition at the location where thedata from the first sweep is joined to data from the second sweep.

FIG. 47 shows an embodiment of the present invention possibly comprisinga single VCSEL source or N VCL sources and a reference signal generator4720. The clocking interferometer and clock box 4705 are integrated intothe light source unit, although they do not have to be. The light sourceunit outputs light to an imaging interferometer 4715 and imagingdetector. The light source also outputs electrical signals for thereference signals, the optical k-clock signal, and the trigger signal.The digitizer subsystem receives the sample signals, the referencesignals, the optical k-clock signal, and the trigger signal. The signalfrom the reference signal generator is acquired with a digital input ofthe digitizer subsystem and used for proper phase, wavelength, orwavenumber alignment. The digital input eliminates the cost of a secondanalog to digital converter. The reference signal comprises an etalon orFabry-Perot filter, an FBG, or any of the alternate reference signalgenerators described in this document. Other reference signal generatorscan be used. In one embodiment, the present invention is used to alignthe wavelength sweeps from a first and a second VCL. In anotherembodiment, the present invention is used to align the wavelength sweepsfrom a first and a second VCL and to align sequential wavelength sweepsfrom both VCLs to phase stabilize the wavelength combined sweeps to eachother.

FIG. 47 alternately shows an embodiment of the present inventioncomprising a single VCL source. In one embodiment, the present inventionis used to align sequential wavelength sweeps from a single VCL sourceor wavelength swept source to phase stabilize the wavelength sweeps.

It is known that interferometers and optical filters can havesensitivity to polarization. Thus, it is possible for an interferometerto have different path lengths for different polarization states or foroptical filters to have different reflectivity or transmission fordifferent polarization states, which would generate an error in thealignment between any two sweeps. In order to facilitate properalignment from different VCL sources or other wavelength swept sources,it can be beneficial to align the polarization states of the VCL sourcesor other sources to be similar. Further, as shown in FIG. 47, it can behelpful to insert a polarization selective optical element 4725, 4730after the VCL source or other wavelength swept source and before thereference signal generator and possibly also before the optical systemor imaging interferometer to ensure similar incident polarization state.Polarization selective optical elements include, but are not limited to:thin film polarizers, wire grid polarizers, dichroic film polarizers,polarizing beam splitters, crystal based polarizers, and polarizers inPIC or PLC devices or other polarization elements known in the art ofoptics. A polarization sensitive gain material or polarization sensitiveamplifier, such as a booster optical amplifier (BOA) can also be usedfollowing the VCL sources to help align the polarization state. Oneembodiment of the present invention further comprises at least onepolarization selective element located after the first VCL source andthe second VCL source and before either the reference signal generatoror optical system or both.

It should be recognized that the electrical trigger signal is often notabsolutely required as the reference signal generator can containsimilar information about the time position of the sweep. For example,if the reference signal generator is an FBG, then it is possible toeliminate the physical trigger connection by using the pre and posttrigger acquisitions methods shown in FIGS. 41A-41C acting on thereference signal. Thus, the reference signal effectively both triggersthe digitizer subsystem and acts to stabilize or align theinterferometric phase, wavelength, or wavenumber of a first wavelengthsweep and a second wavelength sweep. The digitizer subsystem may processthe incoming reference signal from more complex reference signals tofind a characteristic match or signal timing associated with a region ofthe sweep and use the pre and post trigger methods to select the recordof data that contains the sweep. Since an electrical trigger connectionis not very expensive and electrical trigger can reduce thecomputational burden for rough sweep alignment.

FIGS. 48A-48D show schematic diagrams of different embodiments of thepresent invention comprising more than two VCL sources. FIG. 48A showsan embodiment of the present invention comprising an N×1 optical switch.The N×1 optical switch selects between the light from the N VCL sourcesand directs the light from the selected VCL source to the instrument.Not shown are optional optical amplifiers, isolators, and optical tapsfor monitoring, diagnostics, or auxiliary functions. FIG. 48B shows anembodiment of the present invention comprising a wavelength divisionmultiplexer (WDM). Wavelength division multiplexers can be used tocombine or separate light with different wavelengths. However, WDMsoperate best when there is separation between the two wavelength bandsof light. While it is not optimal to use a WDM to combined light fromtwo closely spaced or overlapping spectra, a WDM can be effective usedin the present invention as follows. A first VCL source with shortwavelength range, VCL Source 1, is connected to the short wavelengthinput of a WDM. A second VCL sources with longer wavelength range, VCLSource 2, is connected to a first input of a fiber coupler. A third VCLsource, VCL Source 3, with longer wavelength range than VCL Source 1 orVCL Source 2 is connected to the long wavelength input of the WDM. Thewavelength range of VCL Source 1 and VCL Source 3 is separated by thewavelength range of VCL Source 2, making effective use of the WDM. Theoutput of the WDM is connected to a second input of the fiber coupler.Not shown are optional optical amplifiers, isolators, and optical tapsfor monitoring, diagnostics, or auxiliary functions. FIG. 48C shows anembodiment of the present invention comprising four VCL sources, twoWDMs, and an optical switch. This embodiment of the present invention isdesirable because of low power loss from each VCL source to theinstrument input. A first VCL source, VCL Source 1, is connected to ashort wavelength input of a first WDM. A third VCL source, VCL Source 3,is connected to the long wavelength input of the first WDM. A second VCLsource, VCL Source 2, has longer wavelength range than VCL Source 1, butshorter wavelength range than VCL Source 3 and is connected to the firstinput of a second WDM. A fourth VCL source, VCL Source 4, has thelongest wavelength range and is connected to the second input of thesecond WDM. The output of the first WDM and the second WDM are connectedto a 2×1 optical switch. Not shown are optional optical amplifiers,isolators, and optical taps for monitoring, diagnostics, or auxiliaryfunctions. FIG. 48D shows an embodiment of the present inventioncomprising two VCL Sources and a WDM. VLC Source 1 is connected to oneinput of the WDM and VCL Source 2 is connected to the other input of theWDM.

FIGS. 49A-49D show schematic drawings and plots of differentarrangements of embodiments of the present invention. FIG. 49A shows twoVCL sources with optical outputs combined with a coupler. A portion ofthe light goes to an instrument and another portion of the light goes tomonitoring, diagnostics, and auxiliary functions. As illustrated in FIG.49B, the two VCL sources sweep different, but overlapping wavelengthranges. In this example, the first VCL source sweeps 813 nm to 877 nmand the second VCL source sweeps 873 nm to 937 nm, producing 4 nm ofoverlap. A reference signal generator acting near 875 nm generates areference signal to be used to align the information in the two sweeps.FIG. 49C shows three VCL sources with optical outputs combined with aWDM and a coupler. A portion of the light goes to an instrument andanother portion of the light goes to monitoring, diagnostics, andauxiliary functions. As illustrated in FIG. 49D, the three VCL sourcessweep different wavelength ranges with overlap between the wavelengthranges of the first and second VCL sources and the second and third VCLsources. In this example, the first VCL source sweeps 773 nm to 837 nm,the second VCL source sweeps 833 nm to 897 nm, and the third VCL sourcesweeps 893 nm to 957, producing 4 nm of overlap between adjacent sweeps.A reference signal generator acting near 835 nm generates a referencesignal to be used to align the information in the first and secondsweeps and a reference signal generator acting near 895 nm generates areference signal to be used to align the information in the second andthird sweeps using the methods previously described. Multiple steps ofjoining the data would be performed. The end of the first sweep would bealigned to the start of the second sweep with a correspondence search ofthe present invention, and then the start of the third sweep aligned tothe end of the second sweep with a correspondence search of the presentinvention. The ordering of the joining and aligning of sweeps does notmatter as the resulting sweeps will be properly phase, wavelength, orwavenumber aligned at the completion of the alignment process. Inanother embodiment comprising two etalons or Fabry-Perot filters ofdifferent length, the reference signal generators do not have to beplaced at any particular wavelength as the reference signal generator iseffective over different regions of the sweep.

High Repetition Rate Mode of Operation

FIGS. 50A-50D show a mode of high repetition rate imaging. Two or moreVCL sources are operated in an interleaved mode with spectral overlap,as shown in FIG. 50A. The methods of wavelength, wavenumber, or phasematching taught in the present application are applied to the sweep datato properly align the data with respect to interferogram phase,wavelength, or wavenumber. Once aligned, instead of combining the sweepsinto a single aligned sweep, each of the aligned first wavelength sweepand the second wavelength sweep are processed separately. Numericalapodization can be applied to advantageously shape the sweep envelope,as shown in FIG. 50B. There are now three potential sets of sweep data:the sweep data from the first sweep, the sweep data from the secondsweep, and the sweep data from the combined sweep, as shown in FIG. 50C.The OCT point spread functions for the individual sweeps and thecombined sweep are shown in FIG. 50D. In this mode of operation, theaxial scan rate of the instrument can be effectively increased whencompared to the axial scan rate of any one individual VCL source alone.In the increased speed mode of operation, the axial resolution isdefined by the bandwidth of each of the individual VCL sources. In themode of the combined sweep with bandwidth defined by VCL source 1 andVCL source 2, the axial resolution is defined by the bandwidth of thecombined sweeps and is thus greatly improved. Consequently, high speedOCT data and high resolution data can be obtained in a singleacquisition. In one embodiment of the present invention the opticalinstrument applies OCT processing steps to the sample digital data forthe first wavelength sweep and the sample digital data for the secondswept wavelength sweep separately to increase the A-scan rate of theoptical instrument.

One embodiment of the present invention is a method comprising applyingOCT processing steps to the sample digital data for the first sweep andto the sample digital data for the second sweep separately to increasethe A-scan rate of the optical instrument. The high speed (increasedA-scan rate data) can be processed into OCT data to achieve high spatialsampling rate data, that is particularly suitable for enfacevisualization, including intensity OCT data, Doppler OCT data, andangiography data. The high resolution data from the combined sweeps isparticularly suitable for cross sectional image viewing of data.

FIG. 51 shows a diagram of an example embodiment of the presentinvention that comprises an imaging interferometer 5110, a calibrationinterferometer 5120, and reference signal generator 5130. The signalsfrom the imaging interferometer and calibration interferometer areacquired by two analog to digital converters 5115, 5125. The signal fromthe reference signal generator is acquired by a digital input that issimultaneously clocked with the analog to digital converters. FIG. 51shows an optional optical k-clock 5140 and an optional internal clock5145.

One embodiment of the present invention is an optical instrumentcomprising a wavelength swept source configured for generating tunedemission over a wavelength range to generate a first wavelength sweep ata first time point and a second wavelength sweep at a second time point;an optical system configured for delivering at least a portion of thefirst wavelength sweep and at least a portion of the second wavelengthsweep to a sample and a reference signal generator configured forreceiving at least a portion of the tuned emission from the firstwavelength sweep to generate a reference signal for the first wavelengthsweep and at least a portion of the tuned emission from the secondwavelength sweep to generate a reference signal for the secondwavelength sweep and a sample detector configured for detecting tunedemission from the first wavelength sweep that is affected by the sampleto generate a sample signal for the first wavelength sweep and tunedemission from the second wavelength sweep that is affected by the sampleto generate a sample signal for the second wavelength sweep; an opticalclock generator configured for receiving a portion of the tuned emissionfrom the wavelength swept source to generate a clock signal and adigitizer subsystem configured for converting the sample signal from thefirst wavelength sweep into a sample digital data for the firstwavelength sweep, the sample signal for the second wavelength sweep intoa sample digital data for the second wavelength sweep, the referencesignal for the first wavelength sweep into a reference digital data forthe first wavelength sweep, and the reference signal for the secondwavelength sweep into a reference digital data for the second wavelengthsweep, wherein the clock signal clocks the digitizer subsystem; andwherein the digitizer subsystem further comprises either: (a) a primaryanalog to digital converter, wherein the primary analog to digitalconverter is clocked by the clock signal, and wherein the primary analogto digital converter is configured to convert the sample signal for thefirst wavelength sweep into the sample digital data for the firstwavelength sweep and the sample signal for the second wavelength sweepinto the sample digital data for the second wavelength sweep and acircuit comprising a digital input, wherein the circuit is configure toacquire via the digital input and convert the reference signal for thefirst wavelength sweep into the reference digital data for the firstwavelength sweep and the reference signal for the second wavelengthsweep into the reference digital data for the second wavelength sweep;and wherein the digital input is substantially simultaneously clockedwith the primary analog to digital converter or a frequency multipliedor divided copy of the clock signal; or (b) a primary analog to digitalconverter, wherein the primary analog to digital converter is clocked bythe clock signal, and wherein the primary analog to digital converter isconfigured to convert the sample signal for the first wavelength sweepinto the sample digital data for the first wavelength sweep and thesample signal for the second wavelength sweep into the sample digitaldata for the second wavelength sweep and a secondary analog to digitalconverter, wherein the secondary analog to digital converter isconfigured to convert the reference signal for the first wavelengthsweep into the reference digital data for the first wavelength sweep andthe reference signal for the second wavelength sweep into the referencedigital data for the second wavelength sweep and wherein the secondaryanalog to digital converter is substantially simultaneously clocked withthe primary analog to digital converter or a frequency multiplied ordivided copy of the clock signal and an alignment processor configuredfor using the reference digital data for the first wavelength sweep andthe reference digital data for the second wavelength sweep as input toprocess the sample digital data for the first wavelength sweep and thesample digital data for the second swept wavelength sweep to generateoutput digital data, wherein the resulting output digital data isaligned with respect to at least one of: wavelength, wavenumber, andinterferometric phase to wavelength, wavenumber or phase stabilize thefirst wavelength sweep to the second wavelength sweep. As previouslydescribed, encoding the reference signal with a reference signalgenerator that generates multiple digital state transitions or multipleanalog level transitions per sweep can improve the robustness of thematching to noise. One embodiment of the present invention operates withthe reference digital data for the first wavelength sweep and thereference digital data for the second wavelength sweep containingmultiple level transitions and the alignment processor uses the multiplelevel transitions as input to improve robustness of the alignmentAnother embodiment of the present an optical instrument comprising: awavelength swept source configured for generating tuned emission over awavelength range to generate a first wavelength sweep at a first timepoint and a second wavelength sweep at a second time point and anoptical system configured for delivering at least a portion of the firstwavelength sweep and at least a portion of the second wavelength sweepto a sample and a reference signal generator configured for receiving atleast a portion of the tuned emission from the first wavelength sweep togenerate a reference signal for the first wavelength sweep and at leasta portion of the tuned emission from the second wavelength sweep togenerate a reference signal for the second wavelength sweep; a phasecalibration generator configured for receiving at least a portion of thetuned emission from the first wavelength sweep to generate a phasecalibration signal for the first wavelength sweep and at least a portionof the tuned emission from the second wavelength sweep to generate aphase calibration signal for the second wavelength sweep and a sampledetector configured for detecting tuned emission from the firstwavelength sweep that is affected by the sample to generate a samplesignal for the first wavelength sweep and tuned emission from the secondwavelength sweep that is affected by the sample to generate a samplesignal for the second wavelength sweep and a clock source configured forgenerating a clock signal and a digitizer subsystem configured forconverting the sample signal from the first wavelength sweep into asample digital data for the first wavelength sweep, the sample signalfor the second wavelength sweep into a sample digital data for thesecond wavelength sweep, the reference signal for the first wavelengthsweep into a reference digital data for the first wavelength sweep, thereference signal for the second wavelength sweep into a referencedigital data for the second wavelength sweep, the phase calibrationsignal for the first wavelength sweep into a phase calibration digitaldata for the first wavelength sweep, and the phase calibration signalfor the second wavelength sweep into a phase calibration digital datafor the second wavelength sweep; wherein the clock signal clocks thedigitizer subsystem, and wherein the digitizer subsystem furthercomprises: (a) a primary analog to digital converter, wherein theprimary analog to digital converter is clocked by the clock signal, andwherein the primary analog to digital converter is configured to convertthe sample signal for the first wavelength sweep into sample digitaldata for the first wavelength sweep and the sample signal for the secondwavelength sweep into sample digital data for the second wavelengthsweep and (b) a circuit comprising a digital input, wherein the digitalinput sampling is clocked by the clock signal or a frequency multipliedor divided copy of the clock signal, and wherein the circuit isconfigured to acquire via the digital input and convert the referencesignal for the first wavelength sweep into reference digital data forthe first wavelength sweep and the reference signal for the secondwavelength sweep into reference digital data for the second wavelengthsweep and (c) a secondary analog to digital converter, wherein thesecondary analog to digital converter is clocked by the clock signal ora frequency multiplied or divided copy of the clock signal; and whereinthe secondary analog to digital converter is configured to convert thephase calibration signal for the first wavelength sweep into phasecalibration digital data for the first wavelength sweep and the phasecalibration signal for the second wavelength sweep into phasecalibration digital data for the second wavelength sweep; and analignment processor configured for using the reference digital data forthe first wavelength sweep, the phase calibration digital data for thefirst wavelength sweep, the reference digital data for the secondwavelength sweep, and the phase calibration digital data for the secondsweep as input to process the sample digital data for the firstwavelength sweep and the sample digital data for the second sweptwavelength sweep to generate output digital data, wherein the resultingoutput digital data is aligned with respect to at least one of:wavelength, wavenumber, and interferometric phase to wavelength,wavenumber, or phase stabilize the first wavelength sweep to the secondwavelength sweep. In one embodiment, the clock source comprises anoptical k-clock generator. In another embodiment, the clock sourcecomprises an internal clock generator.

One embodiment of the present invention operates with the referencedigital data for the first wavelength sweep and the reference digitaldata for the second wavelength sweep containing multiple leveltransitions and the alignment processor uses the multiple leveltransitions as input to improve robustness of the alignment. Multiplelevel transitions can occur, for example from an etalon, a Fabry-Perotfilter, an interferometer, multiple Bragg gratings, or an optical filterwith several notch or bandpass regions, for example, or thresholdedsignals thereof to make a digital signal.

There is significant leniency in selecting the fringe frequency of anMZI signal used for phase calibration. The fringe frequency should besignificantly larger than DC so that the fringe contains enough cyclesfor the Hilbert to operate, but frequencies near Nyquist are alsochallenging to effectively use a Hilbert transform because there are sofew samples per cycle and also because the range of frequencies spannedby the MZI fringe, if not perfectly linearized, becomes larger inproportion to the peak fringe frequency, which makes application of theHilbert transform challenging. As a very rough guide, setting the MZIpeak fringe frequency at about 0.05 to 0.5 the Nyquist supported analogfrequency works, with 0.25 the Nyquist supported analog frequency oftenworking well. It is possible to digitize the MZI calibration fringe at alower frequency than the sample data if it is appropriately bandwidthlimited. FIG. 52 shows an example embodiment in which a slow analog todigital converter 5220 digitizes the signal from a calibrationinterferometer and at least one fast analog to digital converter 5210digitizes the signal from the sample interferometer. Using a sloweranalog to digital converter can reduce overall cost and data transferrequirements. One embodiment of the present invention operates with theprimary analog to digital converter sampling at a faster rate than thesecondary analog to digital converter.

Certain modes of OCT require more than one channel of signalacquisition, such as polarization sensitive OCT and complex conjugate(extended depth range) OCT, among others. Since many fast analog todigital converters are available with dual channels, the OCT signal datacan be digitized by a dual channel fast analog converter and thereference interferometer signal digitized by a slower analog to digitalconverter for a significant cost and data transfer savings. The sloweranalog to digital converter can be synchronized to clock on every secondclock cycle of the faster analog converter, as could be implemented witha clock dividing circuit or counting circuit. Other rates ofdigitization or clock division are also possible, such as clocking theslower analog to digital converter every third, fourth, fifth, etc.clock cycle as the fast analog to digital converter. Some analog todigital converters allow dual edge sampling, where a sample is acquiredon every rising or falling edge of the clock cycle, which also allowsanalog to digital converters to be clocked at different rates with thesame clock source. Frequency multiplying circuits, frequency dividingcircuits, and phase locked loop (PLL) circuits also allow generatingclocks of different ratios of slow to fast conversion rate and can beimplemented. One embodiment of the present invention comprises a firstanalog to digital converter acquiring a sample signal at a faster ratethan a second analog to digital converter acquiring the reference signalgenerator signal. One embodiment of the present invention operates withthe primary analog to digital converter sampling at a faster rate thanthe secondary analog to digital converter.

Instrument Architectures

The essential elements of the present invention have been described. Itis possible to arrange the essential elements of the present inventionin a variety of system architectures. For example, FIGS. 53A-53D showseveral possible embodiments of the present invention. In FIG. 53A, asubsystem labeled with (1) comprises VCL source 1 and VCL source 2 in alight source module. The light source module could be an originalequipment manufacturer (OEM) module, a benchtop light source product, anelectronics board with integrated light sources, or other. Light fromthe light source module is directed to an optical system and referencesignal generator that are external to the light source module. Adetection subsystem labeled with (2) comprises the sample detector, thedigitizer subsystem, and the alignment processor. The elements relatedto (2) may reside on the same electronics board or be separate unitswith wire, optical, or wireless communications. The sample detectorcould be constructed with photodiodes and electronic amplifiers. Thedigitizer subsystem comprises an analog to digital converter and A/Dcontroller, as described before. The analog to digital converter may beseparate from the A/D controller, or the analog to digital converter maybe integrated into the A/D controller. The alignment processor could bean FPGA, ASIC, microcontroller, DSP, or any other processing unit. It ispossible to separate the A/D controller and the alignment processor intodifferent logic or computation units, for example, but not limited to:an FPGA plus a processor, two FPGAs, two processors, and an ASIC andprocessor, etc. Further, any processing unit may have multiple cores. Itis also possible that a single FPGA, ASIC, DSP, or a single processor ofany kind could act as the A/D controller and the alignment processor, asshown in FIG. 53B. The controlling of the analog to digital converterand the alignment may exist as different portions of logic or differentportions of software code running or operating on the same processing orlogic unit. In an alternate embodiment, the reference signal generatoris integrated into the light source module, as shown in FIG. 53C. Thishas the advantage for OEM integrators of a simplified interface anddesign. The digitizer subsystem may have an FPGA, ASIC, DSP, orprocessor acting as the A/D controller. The alignment processor could bea PC computer, the processor of a PC computer, a GPU in a PC computer,or any other computational unit. The digitizer subsystem may communicatewith the PC computer via any one of a number of bus and communicationmethods, including, but not limited to: PCIe, PCI, USB, Ethernet, etc.FIG. 53C shows the digitizer subsystem and the alignment processor asdifferent units. FIG. 53D shows a more fully integrated embodiment ofthe present invention. The VCL sources, reference signal generator,sample detector, digitizer subsystem, and alignment processor are allintegrated into a unit. A user or systems integrator of the presentinvention supplies the optical system and sample. This more integratedembodiment of the present invention would be highly desirable for OEMcustomers wanting a simple and comprehensive set of capabilities andfunctionalities that can be used with a wide variety of applicationswith minimal custom development. These specific examples help illustratedifferent architectures of the invention, but are not comprehensive.Very many other approaches for partitioning the essential elements ofthe present invention are possible while still staying within the scopeof the invention.

FIGS. 54A-54C show examples of embodiments of the present invention inwhich the output digital data is further processed, stored, ortransmitted. In FIG. 54A, the output digital data is directed to aninstrument processor. The instrument processor processes the outputdigital data into instrument data. In the case of OCT, the instrumentprocessor takes the output digital data as input and processes theoutput digital data into OCT data. In the case of spectroscopy, theinstrument processor takes the output digital data as input andprocesses the output digital data into spectroscopy data. The instrumentprocessor could be a PC, a processor in a PC, a GPU in a PC, a processorin an instrument, and FPGA in an instrument, an ASIC in an instrument,or any other logic or processor. The instrument data is then directed toany one or combination of being: stored, transmitted, displayed, orfurther processed according to the instrument requirements. In FIG. 54B,a single processor, FPGA, ASIC, GPU, or other processor acts as both thealignment processor and the instrument processor. The alignmentprocessing could be associated with a part of a software program and theinstrument processing could be associated with different part of theprogram, both running on the same essential computational unit. Theresulting instrument data could be directed to any one or anycombination of being: saved, displayed, further processed, transmitted,or analyzed. For example, the instrument data could be any one orcombination of: intensity OCT data, Doppler OCT data, angiography OTCdata, and spectroscopic OTC data. The instrument data could be used inthe context of medical care, such as ophthalmology, cardiology,dermatology, and endoscopy. In one embodiment of the present, the samplecomprises at least one of or any combination of: human tissue, animaltissue, in-vivo tissue, and ex-vivo tissue. In another embodiment of thepresent invention, the sample comprises at least one of or anycombination of: an eye, a portion of an eye, a retina, a crystallinelens, and a cornea. In another embodiment of the present invention, thesample comprises at least one of or any combination of: intravascularplaque, blood vessel, and a stent. In another embodiment of the presentinvention, the sample comprises tissue and the optical instrument isused as part of a process to detect or monitor cancer. The OCT datacould also be used for industrial applications, such as metrology, andquality assurance. While the invention has been primarily described inthe context of OCT, the same wavelength, wavenumber, and signal phasealignment approach can be applied in spectroscopy. In another embodimentof the present invention, the sample comprises at least one of or anycombination of: a gas, solid, liquid, and plasma. As shown in FIG. 52C,it is also possible to direct the output digital data to be any one orany combination of being stored, transmitted, or displayed. The datacould be stored in memory, in non-volatile memory, to tape, to disk, toRAID storage, to cloud storage, to a server, or any other storagedevice. The data could also be transmitted. The transmission of datacould be over a network, via electrical signals, via optical signals,via electromagnetic signals, or any other method of transmitting data.

Different applications of OCT require different wavelengths for optimalperformance. It is known that longer wavelengths exhibit less scatteringin tissue and other materials than shorter wavelengths. Scattering isnot the only consideration when choosing the appropriate wavelength forOCT imaging. Water absorption can attenuate the light signal in thesample and regulatory safety standards limit the maximum exposureallowed on the sample for in vivo imaging. The water absorption windowsaround 850 nm and 1065 nm are often selected for OCT imaging of thehuman retina where the light beam must traverse a round trip throughapproximately 20-25 mm of water in the vitreous. Wavelengths longer thanaround 1100 nm are not commonly used for retinal imaging because thewater absorbs too much light power. Traditionally, wavelengths shorterthan 750 nm have been rarely used for ophthalmic OCT imaging becauseANSI standards limit the light exposure allowed on the eye to smallpower levels at these wavelengths, light is highly scattered at thesewavelengths, and the OCT beam is visible to the patient such that thepatient often tracks the beam as he or she is being scanned, introducingmotion artifacts into the image data. Nevertheless, visible wavelengthOCT has been performed and is of interest for medical diagnosticsbecause of the different contrast obtained at these shorter wavelengths.Thus, OCT systems operating in the visible spectrum are of interest.Infrared light beyond the visible is particularly useful for OCT imagingbecause of reduced scattering at longer wavelengths. Infrared light isalso less visible or not visible to the patient, so the patient is lesslikely to unintentionally follow or track an infrared beam projected onthe eye or retina. Because water absorption starts to increase around900 nm and peaks around 970 nm, the low absorbing windows of infraredlight approaching this absorption peak is particularly useful for OCTimaging. Nearly all commercial retinal OCT imaging instruments operatedwith wavelengths in the 800 nm range. A second water absorption windowexists around 1065 nm. OCT imaging at 1065 nm has been demonstrated toachieve increased penetration into the choroid and optic nerve head ofthe retina and be less susceptible to cataracts when imaging olderpatients. Regulatory standards allow larger power into the eye at 1065nm wavelengths than at 800 nm wavelengths. When imaging skin samples andretinal samples, different contrast has been observed between 1065 nmand 800 nm wavelengths. An OCT imaging system using wavelengths centeredaround 1065 nm and spanning the width of the water absorption window isuseful for OCT imaging. OCT imaging of skin and other scattering tissueand material samples is commonly performed using 1310 nm wavelengths.OCT has also been performed at 1550 nm wavelengths. Recent researchresults have indicated that OCT at longer wavelengths is of interest forOCT. As the wavelength increases, a larger wavelength sweep is requiredto achieve comparable OCT axial resolution. Thus, shorter wavelengthsare often used and preferred for fine resolution OCT imaging and longerwavelengths are often used and preferred for deep penetration OCTimaging through scattering tissue and materials. The 1800-2500 nm rangeis of particular importance for gas spectroscopy. VCLs in this range canbe made with compressively strained InGaAS quantum wells on IndiumPhosphide substrates. VCLs can be designed to operate at all of thesewavelengths. In one embodiment of the present invention, at least oneVCL sweeps through at least one wavelength that is in the range of 750nm-950 nm. In another embodiment of the present invention, at least oneVCL sweeps through at least one wavelength that is in the range of 1000nm-1100 nm. In another embodiment of the present invention, at least oneVCL sweeps through at least one wavelength that is in the range of 1250nm-1700 nm. In another embodiment of the present invention, at least oneVCL sweeps through at least one wavelength that is in the range of 1800nm-2500 nm.

One embodiment of the present invention is a method for aligning digitaldata representing optical measurements from a sample comprising:generating a first wavelength sweep from the tuned emission of a firstVCL source; and generating a second wavelength sweep from the tunedemission of a second VCL source; and directing at least a portion of thefirst wavelength sweep and at least a portion of the second wavelengthsweep towards a sample to generate a first wavelength sweep affected bythe sample and a second wavelength sweep affected by the sample; anddetecting the first wavelength sweep affected by the sample to generatea sample signal for the first wavelength sweep; and detecting the secondwavelength sweep affected by the sample to generate a sample signal forthe second wavelength sweep; and directing at least a portion of thefirst wavelength sweep and at least a portion of the second wavelengthsweep towards a reference signal generator; and generating a referencesignal for the first wavelength sweep from the portion of the firstwavelength sweep with the reference signal generator; and generating areference signal for the second wavelength sweep from the portion of thesecond wavelength sweep with the reference signal generator; andconverting the sample signal for the first wavelength sweep into sampledigital data for the first sweep; and converting the sample signal forthe second wavelength sweep into sample digital data for the secondsweep; and converting the reference signal for the first wavelengthsweep into reference digital data for the first sweep; and convertingthe reference signal for the second wavelength sweep into referencedigital data for the second sweep; and computing a set of alignmentparameters with an alignment processor, wherein the computing uses thereference digital data for the first sweep and the reference digitaldata for the second sweep as input; and generating output digital datarepresenting the sample from the sample digital data for the first sweepand the sample digital data for the second sweep, wherein the outputdigital data is generated using the set of alignment parameterspreviously computed as input, and wherein the resulting output digitaldata is aligned with respect to at least one of: wavelength, wavenumber,and interferometric phase. The method may further comprise computing,with the alignment processor, a correspondence match between a subset ofdata from the reference digital data for the first wavelength sweep anda subset of data from the reference digital data for the secondwavelength sweep or between a subset of data derived from the referencedigital data for the first wavelength sweep and a subset of data derivedfrom the reference digital data for the second wavelength sweep togenerate the set of alignment parameters. The method may comprise tuningthe emission of at least one of the first VCL source and the second VCLsource with a MEMS actuator or a piezo actuator. The method may compriseoperating at least one of the first VCL source and the second VCL sourceunder different modes of operation, wherein the modes of operationdiffer in at least one of sweep repetition rate, sweep wavelength range,sweep center wavelength, and sweep trajectory. The method may compriseprocessing the output digital data into optical coherence tomographydata. The method may comprise processing the output digital data intospectroscopy data. The method may comprise directing at least a portionof the tuned emission of the first wavelength sweep and at least aportion of the tuned emission of the second wavelength sweep through areference Fabry-Perot filter to produce filtered emission for the firstand the second wavelength sweeps, respectively and detecting filteredemission from the first and the second wavelength sweeps to generatereference signals for the first and second wavelength sweeps,respectively, in the reference signal generator. The method may comprisedirecting at least a portion of the tuned emission of the firstwavelength sweep and at least a portion of the tuned emission of thesecond wavelength sweep through a reference interferometer to produceinterfered emission for the first and the second wavelength sweeps,respectively and detecting interfered emission from the first and thesecond wavelength sweeps to generate reference signals for the first andsecond wavelength sweeps, respectively, in the reference signalgenerator. The method may comprise directing at least a portion of thetuned emission of the first wavelength sweep and at least a portion ofthe tuned emission of the second wavelength sweep through a reference aBragg grating or a fiber Bragg grating to produce filtered emission forthe first and the second wavelength sweeps, respectively and detectingfiltered emission from the first and the second wavelength sweeps togenerate reference signals for the first and second wavelength sweeps,respectively, in the reference signal generator. The method may comprisedirecting at least a portion of the tuned emission of the firstwavelength sweep and at least a portion of the tuned emission of thesecond wavelength sweep through a reference notch filter, a referencediffraction grating, a reference prism, or a reference filter to producefiltered emission for the first and the second wavelength sweeps,respectively and detecting filtered emission from the first and thesecond wavelength sweeps to generate reference signals for the first andsecond wavelength sweeps, respectively, in the reference signalgenerator. The method may comprise directing at least a portion of thetuned emission of the first wavelength sweep and at least a portion ofthe tuned emission of the second wavelength sweep through a firstreference Fabry-Perot filter or reference etalon to produce a firstfiltered emission for the first and the second wavelength sweeps,respectively; and directing at least a portion of the tuned emission ofthe first wavelength sweep and at least a portion of the tuned emissionof the second wavelength sweep through a second reference Fabry-Perotfilter or reference etalon to produce a second filtered emission for thefirst and the second wavelength sweeps, respectively; and detecting,with a first detector, the first filtered emission from the first andthe second wavelength sweeps to generate first reference signals for thefirst and second wavelength sweeps, respectively; and detecting, with asecond detector, the second filtered emission from the first and thesecond wavelength sweeps to generate second reference signals for thefirst and second wavelength sweeps, respectively; and electricallysumming the first and second reference signals for the first and secondwavelength sweeps to generate the reference signals for the first andsecond wavelength sweeps in the reference signal generator. The methodmay comprise directing at least a portion of the tuned emission of thefirst wavelength sweep and at least a portion of the tuned emission ofthe second wavelength sweep through a first reference Fabry-Perot filteror reference etalon to produce a first filtered emission for the firstand the second wavelength sweeps, respectively; and directing at least aportion of the tuned emission of the first wavelength sweep and at leasta portion of the tuned emission of the second wavelength sweep through asecond reference Fabry-Perot filter or reference etalon to produce asecond filtered emission for the first and the second wavelength sweeps,respectively; and detecting, with a first detector, the first filteredemission from the first and the second wavelength sweeps to generatefirst reference signals for the first and second wavelength sweeps,respectively; and detecting, with a second detector, the second filteredemission from the first and the second wavelength sweeps to generatesecond reference signals for the first and second wavelength sweeps,respectively; and converting the first and second reference signals forthe first and second wavelength sweeps into digital data; and performinga logical OR operation on the digital data to generate reference signalsfor the first and second wavelength sweeps in the reference signalgenerator. The method may comprise. The method may comprise directing atleast a portion of the tuned emission of the first wavelength sweep andat least a portion of the tuned emission of the second wavelength sweepthrough a first reference Fabry-Perot filter or reference etalon toproduce a first filtered emission for the first and the secondwavelength sweeps, respectively; and directing at least a portion of thetuned emission of the first wavelength sweep and at least a portion ofthe tuned emission of the second wavelength sweep through a secondreference Fabry-Perot filter or reference etalon to produce a secondfiltered emission for the first and the second wavelength sweeps,respectively; and detecting, with a reference detector, the firstfiltered emission from the first and the second wavelength sweeps togenerate first reference signals for the first and second wavelengthsweeps, respectively and the second filtered emission from the first andthe second wavelength sweeps to generate second reference signals forthe first and second wavelength sweeps, respectively, wherein thereference detector acts to sum the first and second signals for thefirst and second wavelength sweeps to generate reference signals for thefirst and second wavelength sweeps in the reference signal generator.The method may comprise converting the sample signal for the first andsecond wavelength sweep into sample digital data for the first andsecond sweep is performed with substantially equal wavenumber spacingbetween sample points. The method may comprise converting the samplesignal for the first and second wavelength sweep into sample digitaldata for the first and second sweep is performed with predetermined timeinterval spacing between sample points. The method may comprisefiltering with a high pass filter, at least one of: the reference signalfor the first wavelength sweep, the reference signal for the secondwavelength sweep, the reference digital data for the first sweep, andthe reference digital data for the second sweep. The method may compriserepeating the steps to generate a first output digital data and a secondoutput digital data; and aligning the second output digital data to thefirst output digital data to generate a set of phase stabilized outputdigital data. The method may comprise applying OCT processing to thesample digital data for the first sweep and to the sample digital datafor the second sweep separately to increase the A-scan rate of theoptical instrument.

While the present invention has been described at some length and withsome particularity with respect to the several described embodiments, itis not intended that it should be limited to any such particulars orembodiments or any particular embodiment, but it is to be construed withreferences to the appended claims so as to provide the broadest possibleinterpretation of such claims in view of the prior art and, therefore,to effectively encompass the intended scope of the invention.Furthermore, the foregoing describes the invention in terms ofembodiments foreseen by the inventor for which an enabling descriptionwas available, notwithstanding that insubstantial modifications of theinvention, not presently foreseen, may nonetheless represent equivalentsthereto.

The invention claimed is:
 1. A method for generating optical coherencetomography data from a swept source optical coherence tomographyinstrument, the method comprising: generating, with a wavelength sweptsource, tuned emission from a first wavelength sweep at a first timepoint and tuned emission from a second wavelength sweep at a second timepoint; delivering at least a portion of the tuned emission from thefirst wavelength sweep and at least a portion of the tuned emission fromthe second wavelength sweep to a sample; generating a reference signalfor the first wavelength sweep from at least a portion of the tunedemission from the first wavelength sweep and generating a referencesignal for the second wavelength sweep from at least a portion of thetuned emission from the second wavelength sweep; detecting tunedemission from the first wavelength sweep that is affected by the sampleto generate a sample signal for the first wavelength sweep and tunedemission from the second wavelength sweep that is affected by the sampleto generate a sample signal for the second wavelength sweep; generatinga clock signal; converting the sample signal from the first wavelengthsweep into a sample digital data for the first wavelength sweep and thesample signal for the second wavelength sweep into a sample digital datafor the second wavelength sweep with a primary analog to digitalconverter clocked by the clock signal or a frequency multiplied ordivided copy of the clock signal; converting the reference signal forthe first wavelength sweep into a reference digital data for the firstwavelength sweep and the reference signal for the second wavelengthsweep into a reference digital data for the second wavelength sweep witha circuit comprising a digital input, wherein the digital input samplingis clocked by the clock signal or a frequency multiplied or divided copyof the clock signal, and wherein the circuit is configured to acquirevia the digital input; and processing, using the reference digital datafor the first wavelength sweep and the reference digital data for thesecond wavelength sweep as input to process the sample digital data forthe first wavelength sweep and the sample digital data for the secondswept wavelength sweep to generate output digital data, wherein theresulting output digital data is aligned with respect to at least oneof: wavelength, wavenumber, and interferometric phase to wavelength,wavenumber, or phase stabilize the first wavelength sweep to the secondwavelength sweep.
 2. The method of claim 1, wherein the processingfurther comprises: performing a correspondence match between thereference digital data for the first wavelength sweep and the referencedigital data for the second wavelength sweep as a part of the processingto generate the output digital data.
 3. The method of claim 2, whereinthe clock signal is derived from the first wavelength sweep and thesecond wavelength sweep.
 4. The method of claim 2, further comprising:generating a phase calibration signal for the first wavelength sweepfrom at least a portion of the tuned emission from the first wavelengthsweep and generating a phase calibration signal for the secondwavelength sweep from at least a portion of the tuned emission from thesecond wavelength sweep; converting the phase calibration signal for thefirst wavelength sweep into a phase calibration digital data for thefirst wavelength sweep and the phase calibration signal for the secondwavelength sweep into a phase calibration digital data for the secondwavelength sweep with a secondary analog to digital converter, whereinthe secondary analog to digital converter is clocked by the clock signalor a frequency multiplied or divided copy of the clock signal; andselecting a starting phase value and an ending phase value; wherein theprocessing further uses the phase calibration digital data for the firstwavelength sweep, the phase calibration digital data for the secondwavelength sweep, the starting phase value, and the ending phase valueas input to generate the output digital data.
 5. The method of claim 4,wherein the clock signal is generated at substantially equal timeintervals.
 6. The method of claim 4, wherein the wavelength swept sourceis operable under at least two different swept source modes ofoperation, wherein the at least two different swept source modes ofoperation differ in at least one of: sweep repetition rate, sweepwavelength range, sweep center wavelength, and sweep trajectory thatcauses the optical coherence tomography instrument to operate in atleast two different OCT modes that differ in at least one of an imagingrange, a sweep repetition rate, and an axial resolution.
 7. The methodof claim 6, wherein generating the phase calibration signals comprises:directing at least a portion of the tuned emission from the firstwavelength sweep through a calibration interferometer and to acalibration detector configured for generating the phase calibrationsignal for the first wavelength sweep; and directing at least a portionof the tuned emission from the second wavelength sweep through thecalibration interferometer and to the calibration detector configuredfor generating the phase calibration signal for the second wavelengthsweep.
 8. The method of claim 7, wherein the starting phase value andthe ending phase value are selected to stay within the expected phaselimits considering sweep to sweep variation such that any experimentalsweep is expected to span at least a range greater than the differencebetween the ending phase value and the starting phase value and whereinthe starting phase value and the ending phase value may be selected tohave different values for the different swept source modes of operation.9. The method of claim 8, wherein the calibration interferometer is setto a fixed optical path delay.
 10. The method of claim 9, wherein thecalibration interferometer is set so that the peak fringe frequency ofthe calibration fringe is between about 0.05 to 0.5 the secondary analogto digital converter Nyquist supported frequency for the at least twodifferent OCT modes.
 11. A swept source optical coherence tomographyinstrument comprising: a wavelength swept source configured forgenerating tuned emission from a first wavelength sweep at a first timepoint and tuned emission from a second wavelength sweep at a second timepoint; an optical system configured for delivering at least a portion ofthe tuned emission from the first wavelength sweep and at least aportion of the tuned emission from the second wavelength sweep to asample; a reference signal generator configured for receiving at least aportion of the tuned emission from the first wavelength sweep togenerate a reference signal for the first wavelength sweep and at leasta portion of the tuned emission from the second wavelength sweep togenerate a reference signal for the second wavelength sweep; a sampledetector configured for detecting tuned emission from the firstwavelength sweep that is affected by the sample to generate a samplesignal for the first wavelength sweep and tuned emission from the secondwavelength sweep that is affected by the sample to generate a samplesignal for the second wavelength sweep; a clock source configured forgenerating a clock signal; and a digitizer subsystem configured forconverting the sample signal from the first wavelength sweep into asample digital data for the first wavelength sweep, the sample signalfor the second wavelength sweep into a sample digital data for thesecond wavelength sweep, the reference signal for the first wavelengthsweep into a reference digital data for the first wavelength sweep, thereference signal for the second wavelength sweep into a referencedigital data for the second wavelength sweep; wherein the digitizersubsystem further comprises: a) a primary analog to digital converter,wherein the primary analog to digital converter is clocked by the clocksignal or a frequency multiplied or divided copy of the clock signal,and wherein the primary analog to digital converter is configured toconvert the sample signal for the first wavelength sweep into the sampledigital data for the first wavelength sweep and the sample signal forthe second wavelength sweep into the sample digital data for the secondwavelength sweep; and b) a circuit comprising a digital input, whereinthe digital input sampling is clocked by the clock signal or a frequencymultiplied or divided copy of the clock signal, and wherein the circuitis configured to acquire via the digital input and convert the referencesignal for the first wavelength sweep into the reference digital datafor the first wavelength sweep and the reference signal for the secondwavelength sweep into the reference digital data for the secondwavelength sweep; and an alignment processor configured for using thereference digital data for the first wavelength sweep and the referencedigital data for the second wavelength sweep as input to process thesample digital data for the first wavelength sweep and the sampledigital data for the second swept wavelength sweep to generate outputdigital data, wherein the resulting output digital data is aligned withrespect to at least one of: wavelength, wavenumber, and interferometricphase to wavelength, wavenumber, or phase stabilize the first wavelengthsweep to the second wavelength sweep.
 12. The swept source opticalcoherence tomography system of claim 11, wherein the alignment processoris further configured to perform a correspondence match between thereference digital data for the first wavelength sweep and the referencedigital data for the second wavelength sweep as a part of the processingto generate the output digital data.
 13. The optical coherencetomography system of claim 12, wherein the clock source derives theclock signal from the first wavelength sweep and the second wavelengthsweep.
 14. The swept source optical coherence tomography instrument ofclaim 12, further comprising: a phase calibration generator configuredfor receiving at least a portion of the tuned emission from the firstwavelength sweep to generate a phase calibration signal for the firstwavelength sweep and at least a portion of the tuned emission from thesecond wavelength sweep to generate a phase calibration signal for thesecond wavelength sweep; wherein the digitizer further comprises: c) asecondary analog to digital converter, wherein the secondary analog todigital converter is clocked by the clock signal or a frequencymultiplied or divided copy of the clock signal; and wherein thesecondary analog to digital converter is configured to convert the phasecalibration signal for the first wavelength sweep into a phasecalibration digital data for the first wavelength sweep and the phasecalibration signal for the second wavelength sweep into a phasecalibration digital data for the second wavelength sweep; and whereinthe alignment processor is further configured for using the phasecalibration digital data for the first wavelength sweep, the phasecalibration digital data for the second wavelength sweep, a selectedstarting phase value, and a selected ending phase value as part of theprocessing to generate the output digital data.
 15. The swept sourceoptical coherence tomography instrument of claim 14, wherein the clocksignal is generate at substantially equal time intervals.
 16. The sweptsource optical coherence tomography instrument of claim 14, wherein thewavelength swept source is operable under at least two different sweptsource modes of operation, wherein the at least two different sweptsource modes of operation differ in at least one of: sweep repetitionrate, sweep wavelength range, sweep center wavelength, and sweeptrajectory that causes the swept source optical coherence tomographyinstrument to operate in at least two different OCT modes that differ inat least one of an imaging range, a sweep repetition rate, and an axialresolution.
 17. The swept source optical coherence tomography instrumentof claim 16, wherein the phase calibration generator further comprises acalibration interferometer and calibration detector configured forreceiving at least a portion of the tuned emission from the firstwavelength sweep to generate the phase calibration signal for the firstwavelength sweep and at least a portion of the tuned emission from thesecond wavelength sweep to generate the phase calibration signal for thesecond wavelength sweep.
 18. The optical coherence tomography instrumentof claim 17, wherein the starting phase value and the ending phase valueare selected to stay within the expected phase limits considering sweepto sweep variation such that any experimental sweep is expected to spanat least a range greater than the difference between the ending phasevalue and the starting phase value and wherein the starting phase valueand the ending phase value may be selected to have different values forthe different OCT modes of operation.
 19. The optical coherencetomography instrument of claim 18, wherein the calibrationinterferometer is set to a fixed optical path delay.
 20. The opticalcoherence tomography instrument of claim 19, wherein the calibrationinterferometer is set so that the peak fringe frequency of thecalibration fringes is between about 0.05 to 0.5 the secondary analog todigital converter Nyquist supported frequency for the at least twodifferent OCT modes.
 21. A data acquisition system for producing aligneddigital data representing an optical signal comprising: a clockconfigured for generating a clock signal; a primary analog to digitalconverter configured for generating a first sample digital data and asecond sample digital data, wherein the primary analog to digitalconverter is clocked by the clock signal or a frequency multiplied ordivided copy of the clock signal; a circuit comprising a digital input,wherein the digital input sampling is clocked by the clock signal or afrequency multiplied or divided copy of the clock signal, and whereinthe circuit is configured to acquire via the digital input and generatea first reference digital data and a second reference digital data; andan alignment processor configured for performing a correspondence matchbetween the first reference digital data and the second referencedigital data and use the result of the correspondence match, the firstsample digital data, and the second sample digital data as input togenerate output digital data, wherein the resulting output digital datais aligned with respect to at least one of: wavelength, wavenumber, andinterferometric phase to wavelength, wavenumber, or phase stabilize thefirst sample digital data and a second sample digital data.
 22. The dataacquisition system of claim 21, further comprising: a secondary analogto digital converter configured for generating a first phase calibrationdigital data and a second phase calibration digital data, wherein thesecondary analog to digital converter is clocked by the clock signal ora frequency multiplied or divided copy of the clock signal; and whereinthe alignment processor is further configured for using the phasecalibration digital data and the phase calibration digital data as partof the processing to generate the output digital data.